Jimmy Bullard scored a stoppage-time penalty to rescue a point for Fulham.
Bullard was a threat for Fulham with his telling passes
El-Hadji Diouf had given Bolton the lead with a penalty after Luis Boa Morte was adjudged to have fouled Gary Speed as he closed in on a cross.
But in a game of few chances Bullard's strike just squeezed past Jussi Jaaskelainen after Abdoulaye Faye was penalised for handball.
Jaaskelainen had earlier made saves from Brian McBride and Michael Brown while Faye went close for Fulham.
The result means that Bolton are still searching for their first away win in the Premiership since their 4-0 victory at Everton last December.
But after Fulham's 5-1 thrashing at Manchester United on Sunday the point will be gratefully received by Fulham boss Chris Coleman.
In truth it was a poor game that only really came to life after Diouf's 73rd minute goal.
Bolton's only first-half opening came when Ivan Campo picked out an unmarked Kevin Davies but the Bolton striker could not control the ball cleanly with his first touch and Heidar Helguson cleared.
Bullard provided several of the game's few moments of real quality with his delivery from set pieces.
McBride met his curling free kick after 15 minutes but Jaskelainen saved his header, while Ian Pearce could not find the target after another superb ball from Bullard.
A long-range shot from Bullard on the half-hour mark was heading wide but took a wicked deflection off Quinton Fortune and forced another save from Jaaskelainen.
Helguson evaded Nicky Hunt but headed wide after the break, while Brown connected with a Luis Boa Morte cross but Jaaskelainen saved low down.
Fortune, troubled so often by injury at Manchester United, limped off to be replaced by Faye, who almost made an immediate impact with a header that he could not quite keep on target.
A set piece seemed the most likely prospect for a goal and so it proved with Diouf's superbly taken penalty, which he buried in the top corner of the net.
The goal brought the game to life and Ricardo Vaz Te almost doubled Bolton's advantage but could not quite keep his header from Diouf's inviting cross on target.
Tomasz Radzinski came on for Fulham and twice went close with shots, one of them hooked clear by Faye.
But Fulham were not to be denied and after Boa Morte's header struck Faye flush on the arm Bullard restored parity to score his first goal since joining the Cottagers.
Fulham manager Chris Coleman:
"Playing Bolton after being beaten 5-1 you need to show great character and we showed that in bundles.
"We tried to match Bolton with their direct style and we worked hard. We had a real go and tried to win the game.
"We will take many positives into the next game, against Sheffield United."
Bolton manager Sam Allardyce on Abdoulaye Faye's handball:
"It was very unprofessional, very childish. There was no need to do what he did.
"Had he not done that I think that we would have cleared the ball.
"For the last six seasons we have come to Fulham and got nothing. This time we got our noses in front - that's why I am so disappointed not to have won."
Fulham: Niemi, Queudrue, Christanval, Pearce, Rosenior, Brown (Radzinski 81), Diop, Bullard, Boa Morte, Helguson (John 69), McBride.
Subs Not Used: Drobny, Volz, Bocanegra.
Goals: Bullard 90 pen.
Bolton: Jaaskelainen, Hunt, Meite, Ben Haim, Fortune (Pedersen 66), Nolan, Campo, Speed, Vaz Te, Davies (Faye 60), Diouf.
Subs Not Used: Walker, Giannakopoulos, Tal.
Booked: Davies, Diouf, Nolan.
Goals: Diouf 73 pen.
Ref: A Wiley (Staffordshire).