But there was no sign of unfamiliarity as the hosts got off to a pulsating start, flooding forward in numbers and exhibiting a one-touch pass-and-move approach that CSKA struggled to contain.
With full-backs John Pantsil and Stephen Kelly marauding upfield, and Simon Davies and Gera pushing on to support lone-striker Bobby Zamora, Fulham were not short of attacking options and Murphy ensured a steady supply of pinpoint passes.
After CSKA goalkeeper Zdravko Chavdarov reacted well to deny Zamora and Davies, Timonov rattled the woodwork with a venomous left-footed drive - but an opener for the visitors would have come totally against the run of play.
Fulham, full of craft and cohesion, continued to push for a breakthrough and should have had their reward when Gera's surge into the box was ended by Ivanov's hopeless tackle.
Murphy appeared full of confidence as he stepped up but then blasted his spot-kick horribly high.
But CSKA, seemingly low on confidence despite the backing of a large and highly-vocal section of the crowd, failed to make Fulham pay.
Fulham looked set for a comfortable win before CSKA rallied late on
And, moments after Pantsil saw a fizzing effort well-saved, Riise stood up an inviting cross from the right which Vidanov and Ivanov failed to deal with, allowing Gera to race through and head powerfully past Chavdarov.
Zamora ought to have doubled the lead when he volleyed over and another gilt-edged chance went begging as Davies dragged wide from eight yards out.
CSKA came out for the second half with a spring in their step and it looked as though Fulham might have been made to regret their profligacy.
Spas Delev played Todor Yanchev through on goal, only for Kelly to arrive with a last-ditch challenge, before Delev shinned the ball wide following Yordan Minev's right-wing cross.
Hodgson had replaced Brede Hangeland with Aaron Hughes at half-time and Fulham's new centre-half pairing of Hughes and Chris Smalling struggled to gel.
They lacked protection and, with Fulham's midfield now relinquishing possession all too easily, faced wave after wave of CSKA pressure late on.
The visitors' big chance came on 81 minutes when Yanev drilled in a goal-bound effort from 25-yards, but Duff got down to repel it off the line with his knee.
Fulham were resorting to counter-attack football but goalscoring opportunities were few and far between and fatigue began to set in.
Delev zipped a shot just over but, despite spending the last quarter firmly on the back foot, Fulham held on for a vital victory.
Fulham manager Roy Hodgson: "All credit to CSKA, they had nothing to lose in the last 20 minutes and brought talented players on. When you make changes it makes it difficult for players.
"It was foolish to miss a penalty but there were other missed chances and the game could have been dead and buried.
"I'm very pleased that we showed the strength of character to stand up to that."
CSKA Sofia coach Luboslav Penev on missing the first-half: "I arrived 15 minutes before half-time and remained in the tunnel until the break. The most important thing is that I arrived during the game and was close to my assistants and my team.
"I was told about the first 30 minutes, they were fast forgotten and we outplayed Fulham in the second half. This is how I would like my team to play always.
"We deserved a goal and at least a point after creating five or six opportunities. Maybe we should have had a penalty too."
90:00+3:09 The referee blows for the end of the match.
89:52 Unfair challenge on John Pantsil by Spas Delev results in a free kick. Mark Schwarzer takes the free kick.
88:34 Bjorn Helge Riise takes the free kick.
88:34 Booking Kostadin Stoyanov receives a yellow card for unsporting behaviour.
88:29 Kostadin Stoyanov concedes a free kick for a foul on Zoltan Gera.
86:09 Centre by Viktors Morozs, Close range header by Todor Yanchev goes over the bar.
83:05 Effort on goal by Spas Delev from long range goes harmlessly over the bar.
82:09 Marinho Rui Miguel has an effort at goal from outside the area missing to the wide right of the goal.
81:05 Outswinging corner taken by Todor Yanchev, Shot by Kosta Yanev. Blocked by Damien Duff.
80:30 The free kick is delivered right-footed by Spas Delev from left wing, save by Mark Schwarzer.
80:30 Booking The referee cautions John Pantsil for unsporting behaviour.
80:27 Unfair challenge on Apostol Popov by John Pantsil results in a free kick.
77:57 Substitution Damien Duff joins the action as a substitute, replacing Danny Murphy.
77:32 Free kick awarded for an unfair challenge on Iordan Minev by Zoltan Gera. Todor Yanchev restarts play with the free kick.
75:38 Bobby Zamora is ruled offside. Apostol Popov takes the indirect free kick.
73:48 Iordan Minev delivers the ball, blocked by Stephen Kelly. Spas Delev takes a outswinging corner to the near post.
72:28 Mesquita Michel is ruled offside. Indirect free kick taken by Mark Schwarzer.
71:40 Substitution Marinho Rui Miguel on for Yordan Todorov.
69:17 Substitution Clinton Dempsey comes on in place of Simon Davies.
67:16 The referee blows for offside. Zdravko Chavdarov restarts play with the free kick.
66:30 Inswinging corner taken right-footed by Bjorn Helge Riise from the left by-line, Yordan Todorov makes a clearance.
63:40 Foul by Simon Davies on Kostadin Stoyanov, free kick awarded. Free kick crossed by Spas Delev, save made by Mark Schwarzer.
62:38 Substitution Kosta Yanev joins the action as a substitute, replacing Ivan Ivanov.
62:38 Effort by Bjorn Helge Riise from a long way out goes over the target.
61:47 Bjorn Helge Riise crosses the ball in from the free kick, Viktors Morozs manages to make a clearance.
61:47 Booking Booking for Iordan Minev.
61:33 Iordan Minev gives away a free kick for an unfair challenge on Bjorn Helge Riise. Chris Baird takes the free kick. Foul by
Iordan Minev on Bjorn Helge Riise, free kick awarded.
60:57 Unfair challenge on Stephen Kelly by Iordan Minev results in a free kick. Stephen Kelly takes the direct free kick.
58:13 Effort from inside the area by Spas Delev misses to the right of the goal.
57:11 Corner from the right by-line taken by Simon Davies, Aaron Hughes produces a header from deep inside the six-yard box that
clears the bar.
56:16 Corner taken right-footed by Yordan Todorov, Mesquita Michel takes a shot. Save by Mark Schwarzer.
55:18 Unfair challenge on Pavel Vidanov by Zoltan Gera results in a free kick. Pavel Vidanov takes the direct free kick.
54:39 Kostadin Stoyanov crosses the ball.
53:08 Substitution Mesquita Michel comes on in place of Todor Timonov.
51:16 The ball is sent over by Zoltan Gera, clearance made by Ivan Ivanov.
49:58 Bobby Zamora has an effort at goal from deep inside the area missing to the right of the target.
47:50 Foul by Iordan Minev on Zoltan Gera, free kick awarded. Mark Schwarzer takes the free kick.
45:01 The second half kicks off.
45:01 Substitution Aaron Hughes on for Brede Hangeland.
45:00+0:58 The referee calls an end to the first half.
43:34 Inswinging corner taken by Todor Timonov from the right by-line played to the near post, clearance by John Pantsil.
40:24 Todor Yanchev takes the free kick. Todor Timonov takes a shot from a long way out clearing the crossbar.
40:24 Booking Chris Baird goes into the referee's book for unsporting behaviour.
40:21 Free kick awarded for a foul by Chris Baird on Todor Yanchev.
40:01 Viktors Morozs gives away a free kick for an unfair challenge on Danny Murphy. Direct free kick taken by John Pantsil.
38:36 Todor Timonov has an effort at goal from outside the box which goes wide right of the goal.
37:57 Foul by John Pantsil on Todor Timonov, free kick awarded. The free kick is delivered right-footed by Yordan Todorov from left
wing, Mark Schwarzer makes a save.
34:57 Booking Viktors Morozs is shown a yellow card.
34:36 Iordan Minev crosses the ball, clearance made by Chris Baird.
31:29 Unfair challenge on Apostol Popov by Zoltan Gera results in a free kick. Todor Yanchev takes the direct free kick.
29:46 Outswinging corner taken from the right by-line by Simon Davies, Brede Hangeland produces a header from deep inside the six-yard
box that clears the crossbar.
29:24 Free kick awarded for an unfair challenge on Brede Hangeland by Spas Delev. Direct free kick taken by Brede Hangeland.
28:16 Effort from inside the six-yard box by Simon Davies goes wide right of the goal.
26:53 Drilled right-footed shot by Bjorn Helge Riise. Zdravko Chavdarov makes a save.
25:50 Free kick awarded for an unfair challenge on Zoltan Gera by Pavel Vidanov. Simon Davies restarts play with the free kick.
23:55 Simon Davies takes a outswinging corner from the right by-line played to the near post, Apostol Popov makes a clearance. Simon
Davies takes the outswinging corner, Headed effort from deep inside the penalty area by Chris Smalling misses to the left
of the goal.
22:29 The referee blows for offside against Bobby Zamora. Free kick taken by Ivan Ivanov.
20:13 John Pantsil is penalised for a handball. The free kick is delivered left-footed by Todor Timonov from left wing, clearance
made by Zoltan Gera.
18:11 Corner taken by Todor Timonov from the right by-line played to the near post, John Pantsil makes a clearance. Todor Timonov
takes a short corner.
17:41 Corner from the left by-line taken by Yordan Todorov, Stephen Kelly manages to make a clearance.
17:06 Effort on goal by Bobby Zamora from just inside the penalty area goes over the target.
13:59 Assist by Bjorn Helge Riise. The referee blows for offside. Indirect free kick taken by Chris Smalling.
13:59 GOAL - Zoltan Gera:Fulham 1 - 0 CSKA Sofia Zoltan Gera grabs a headed goal from close in. Fulham 1-0 CSKA Sofia.
13:58 Bjorn Helge Riise delivers the ball,
13:29 John Pantsil takes a shot. Save by Zdravko Chavdarov. Simon Davies takes a outswinging corner to the near post, clearance
made by Todor Yanchev.
12:06 Bobby Zamora has an effort at goal from 25 yards. Blocked by Apostol Popov. Corner taken by Bjorn Helge Riise from the left
by-line, save made by Zdravko Chavdarov.
11:08 Free kick awarded for an unfair challenge on Ivan Ivanov by Bobby Zamora. Direct free kick taken by Ivan Ivanov.
10:29 A cross is delivered by Bjorn Helge Riise, Zdravko Chavdarov makes a save.
8:45 Free kick awarded for an unfair challenge on Simon Davies by Kostadin Stoyanov. Chris Smalling takes the direct free kick.
7:24 Penalty taken by Danny Murphy and missed.
7:24 Penalty awarded for an unfair challenge on Zoltan Gera by Ivan Ivanov.
4:42 Todor Timonov takes a shot. Todor Timonov concedes a free kick for a foul on Zoltan Gera. The free kick is delivered right-footed
by Danny Murphy from left channel, save by Zdravko Chavdarov.
3:23 Viktors Morozs challenges Simon Davies unfairly and gives away a free kick. Danny Murphy takes the direct free kick. Simon
Davies takes a shot. Save made by Zdravko Chavdarov.
0:32 The referee blows for offside against Bobby Zamora. Free kick taken by Zdravko Chavdarov.
0:00 The ref blows the whistle to start the match.
Live text and data provided by The Press Association.
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