The Welshmen put their differences aside before the game, but it was Hughes who had cause to celebrate at full-time, thanks largely to the way his side controlled the game, with Danny Murphy particularly dominant in midfield.
Hughes doesn't think red card changed game
For all Stoke's commitment and indefatigable effort, they lacked the guile to unlock the Fulham defence and had to rely on set-pieces to provide their best goalscoring opportunities.
Indeed, it was an early Stoke free-kick that gave the game its first clear effort on goal.
Matthew Etherington's floated ball was met by Shawcross, who headed wide when he should have at least hit the target.
From there Fulham took a firmer footing. Damien Duff, as a prelude to the problems he would cause down the Stoke left, cut inside past Rory Delap and rattled a shot against the visitors' bar from 25 yards out.
With the hosts enjoying the lion's share of possession, Stoke were pushed further back into their own half, but should have taken the lead midway through the first period.
After Murphy was booked for a challenge on Dean Whitehead, the resulting free-kick fell to Jones in the Fulham penalty area.
With goalkeeper David Stockdale scrambling across his line, the former Sunderland man unleashed a right-foot shot that rattled the outside of the post.
Soon after, Stoke were made to pay. Duff's ball into the box found the feet of Johnson, who had been recalled to the Fulham starting line-up after scoring the equaliser in the
1-1 draw with Wigan.
On his 150th Premier League appearance, the former Birmingham and Crystal Palace striker took the long way around Shawcross and from close to the byeline rolled the ball across Asmir Begovic's goal, with Dempsey sliding in front of Andy Wilkinson to finish.
The remainder of the first half passed without incident, but with Fulham continuing to rule the middle of the park, the Potters headed for the dressing room to consider how to provide better service to the front two of Jones and Tuncay.
Whatever plan Pulis put in place to get his side back in the game, it was destroyed early in the second half.
Murphy's exquisite pass from deep found Dempsey, who deftly spun away from Shawcross and Robert Huth and moved towards Begovic's goal.
He was denied the chance to shoot by Shawcross, who grappled him to the ground. The Stoke skipper was dismissed for the challenge and Dempsey rammed the resulting penalty into the middle of the net.
Pulis frustrated by red card for Shawcross
Pulis reshuffled his pack, handing
a debut to striker John Carew,
but the striker on loan from Aston Villa had little impact bar a mazy run into the hosts' box.
An injury to Dickson Etuhu gave Steve Sidwell a first Fulham appearance from the substitutes' bench, as the home side's ability to keep the ball gave Stoke little hope of getting back into the game.
Johnson could have added a third, but he could only shoot at Begovic after skilfully collecting a long ball from Aaron Hughes and fending off the challenge of Abdoulaye Faye. The spurned chance would not prove costly, as Stoke were already beaten.
The win moves Fulham up to 14th in the table, the four-point advantage over the bottom three providing some daylight between themselves and the relegation zone.
Already on 30 points, Stoke drop to ninth but will feel that they are close to safety, even if Pulis has yet to unlock the secret of consistently winning away in the top flight.
74:23 Substitution Moussa Dembele goes off and Zoltan Gera comes on.
73:15 Foul by Damien Duff on Kenwyne Jones, free kick awarded. Free kick taken by Glenn Whelan.
72:28 Inswinging corner taken by Damien Duff from the right by-line, clearance made by Robert Huth.
71:34 Andrew Johnson takes a shot. Save made by Asmir Begovic.
Correction - 68:34 Unfair challenge on Moussa Dembele by Abdoulaye Faye results in a free kick. Danny Murphy takes the direct free kick. Steve
Sidwell takes a shot. Robert Huth gets a block in. Short corner worked by Danny Murphy.
68:34 Foul by Abdoulaye Faye on Moussa Dembele, free kick awarded. Free kick taken by Danny Murphy. Steve Sidwell takes a shot.
Robert Huth gets a block in. Danny Murphy decides to take a short corner.
67:17 Long range shot by Andy Wilkinson goes wide right of the goal.
66:57 Glenn Whelan takes the outswinging corner, Chris Baird manages to make a clearance.
65:50 Danny Murphy fouled by Marc Wilson, the ref awards a free kick. Free kick taken by Danny Murphy.
61:53 Substitution Glenn Whelan replaces Matthew Etherington.
61:53 Substitution Steve Sidwell is brought on as a substitute for Dickson Etuhu.
57:21 Substitution Abdoulaye Faye joins the action as a substitute, replacing Tuncay Sanli.
57:21 Substitution John Carew joins the action as a substitute, replacing Danny Collins.
56:20 Foul by Andy Wilkinson on Dickson Etuhu, free kick awarded. Chris Baird restarts play with the free kick. Dickson Etuhu concedes
a free kick for a foul on Dean Whitehead. Danny Collins restarts play with the free kick.
55:04 GOAL - Clint Dempsey:Fulham 2 - 0 Stoke Power penalty scored by Clint Dempsey. Fulham 2-0 Stoke.
54:01 Penalty awarded for an unfair challenge on Clint Dempsey by Ryan Shawcross.
54:01 Sent off Ryan Shawcross sent from the field by the ref for professional foul.
46:36 Danny Collins concedes a free kick for a foul on Damien Duff. Damien Duff takes the direct free kick.
45:01 The second half begins.
45:00+2:18 The match has reached half-time.
45:00+1:51 Unfair challenge on Danny Collins by Moussa Dembele results in a free kick. Free kick taken by Asmir Begovic.
43:22 Danny Murphy takes a shot. Blocked by Robert Huth.
40:58 Unfair challenge on Danny Murphy by Dean Whitehead results in a free kick. Danny Murphy restarts play with the free kick.
Chris Baird takes a shot.
38:53 Dean Whitehead challenges Damien Duff unfairly and gives away a free kick. Danny Murphy takes the free kick.
37:01 Moussa Dembele challenges Danny Collins unfairly and gives away a free kick. Direct free kick taken by Asmir Begovic.
34:42 Foul by Andy Wilkinson on Andrew Johnson, free kick awarded. Free kick crossed right-footed by Danny Murphy.
34:42 Booking The referee shows Andy Wilkinson a yellow card for unsporting behaviour.
32:53 Assist on the goal came from Andrew Johnson.
32:53 GOAL - Clint Dempsey:Fulham 1 - 0 Stoke A goal is scored by Clint Dempsey from close in low into the middle of the goal. Fulham 1-0 Stoke.
31:10 Tuncay Sanli takes a inswinging corner from the left by-line to the near post, Moussa Dembele manages to make a clearance.
30:28 The referee blows for offside. Free kick taken by Asmir Begovic.
28:01 Foul by Dickson Etuhu on Dean Whitehead, free kick awarded. Free kick taken by Asmir Begovic.
26:55 Shot from outside the box by Marc Wilson goes wide right of the target.
26:08 Free kick awarded for a foul by Dickson Etuhu on Dean Whitehead. Ryan Shawcross takes the direct free kick.
25:06 Shot from inside the six-yard box by Kenwyne Jones hits the post.
24:22 Unfair challenge on Dean Whitehead by Danny Murphy results in a free kick. Direct free kick taken by Robert Huth.
24:22 Booking The referee shows Danny Murphy a yellow card for unsporting behaviour.
Correction - 23:31 Chris Baird takes a shot. Comfortable save by Asmir Begovic.
23:31 Chris Baird takes a shot. Asmir Begovic makes a comfortable save.
22:11 Outswinging corner taken left-footed by Damien Duff from the left by-line, Kenwyne Jones manages to make a clearance.
21:47 Damien Duff takes a shot. Asmir Begovic makes a save.
13:49 Andrew Johnson gives away a free kick for an unfair challenge on Robert Huth. Asmir Begovic takes the direct free kick.
12:16 Tuncay Sanli takes a shot. David Stockdale makes a save.
11:40 The official flags Andrew Johnson offside. Indirect free kick taken by Asmir Begovic.
10:25 Danny Murphy has an effort at goal from outside the area missing to the wide left of the goal.
7:15 John Pantsil gives away a free kick for an unfair challenge on Robert Huth. Asmir Begovic takes the free kick.
6:31 Damien Duff takes a shot. Save by Asmir Begovic.
3:27 Danny Murphy gives away a free kick for an unfair challenge on Dean Whitehead. A cross is delivered by Matthew Etherington,
Headed effort from inside the area by Ryan Shawcross misses to the left of the target.
2:20 Kenwyne Jones concedes a free kick for a foul on Aaron Hughes. David Stockdale restarts play with the free kick.
1:01 Robert Huth produces a headed effort from deep inside the six-yard box which goes wide of the right-hand upright.
0:00 The referee starts the match.
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