Fulham's Heidar Helguson fires into his own net
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Captain Kevin Nolan notched his 10th goal of the season as Bolton came from behind to secure the three points.
Striker Heidar Helguson towered above the Bolton defence to head home Simon Elliot's free-kick on 22 minutes handing Fulham a deserved lead.
But the Cottagers' hero turned villain on the stroke of half time when his attempted clearance found his own net.
The home side were rewarded for their pressure on 68 minutes when Nolan's persistence earned them the victory.
Bolton were keen to banish the memories of their Uefa Cup exit at Marseille on Thursday and stretch their unbeaten league run to seven games.
And Fulham, who lost goalkeeper Antti Niemi through injury in the warm-up, were aiming for their first away victory of the season.
But it was the visitors who made the better start and almost took the lead when Tomasz Radzinski picked out Helguson with a delightful chip only for the Icelandic striker to crash his volley against the crossbar.
Moments later Helguson had a penalty appeal turned down by referee Phil Dowd after a sliding challenge by Radhi Jaidi as Fulham dominated the first half.
Fulham eventually took the lead on 22 minutes when Helguson rose above the Bolton defence to head home Simon Elliot's curling set piece.
Brian McBride could have doubled the advantage just before half time when he found himself unmarked in the penalty area, but Bolton keeper Jussi Jaaskelainen did well to smother at his feet.
Wanderers found it difficult to find any rhythm in the opening 45 minutes and were hurried into mistakes as Abdoulaye Faye, on his 28th birthday, almost deflected a Luis Boa Morte cross into his own net.
However, Bolton did respond on the stroke of half time when a Stelios cross caused confusion among the Fulham defence and Helguson's attempted clearance found the roof of his own net after Tony Warner turned away N'Gotty's header.
The home side started the second half with more purpose and vigour and looked to test the Fulham back-line with an aerial bombardment.
And Bolton's pressure paid off on 68 minutes when Nolan forced his way through some weak tackles in the Fulham defence and coolly slotted past Warner.
Gary Speed was brought on by Bolton boss Sam Allardyce for his 550th appearance in English top flight football to steady the midfield.
But the visitors kept pressing with Papa Bouba Diop and Helguson both wasting good chances to level from unchallenged headers.
And the Cottagers somehow failed to find the net late on when first Steed Malbranque, and then Boa Morte missed in a goalmouth scramble after a fine Jaaskelainen save.
Bolton manager Sam Allardyce:
"I challenged the players after Thursday to hit back with a win. The lads were magnificent and showed great character after that defeat.
"We have to set our goals high and challenge every player to deliver a performance that would get us a win.
"The lads have done that now and we can build on this in the next few weeks."
Fulham manager Chris Coleman:
"We were disappointed coming in at half time at 1-1 as we felt that we should have held the lead on the chances we created.
"In fact, we should have been further ahead going into the break.
"For the first 45 minutes we were the better side but we didn't capitalise on the chances we created and when Bolton got the equaliser they troubled us."
Bolton: Jaaskelainen, O'Brien, N'Gotty, Jaidi, Gardner, Faye (Speed 60), Okocha (Ben Haim 90), Nakata (Vaz Te 82), Nolan, Davies, Giannakopoulos.
Subs Not Used: Walker, Borgetti.
Booked: Nolan.
Goals: Helguson 45 og, Nolan 68.
Fulham: Warner, Volz, Bocanegra, Knight, Bridge, Radzinski (Diop 75), Elliott, Malbranque, Boa Morte, Helguson, McBride (John 75).
Subs Not Used: Rosenior, Goma, Niclas Jensen.
Booked: Boa Morte.
Goals: Helguson 22.
Att: 23,104
Ref: P Dowd (Staffordshire).