The game was virtually settled in the 13th minute when the Londoners had Claus Jensen sent off for handling the ball on the line.
Jay-Jay Okocha fired Wanderers ahead from the penalty spot and Kevin Nolan added a second after 33 minutes to leave Wanderers coasting at half-time.
Fulham, however, gave them a jolt two minutes into the second half when Luis Boa Morte pulled a goal back, but once Stelios Giannakopoulos restored the home side's two-goal cushion after 54 minutes Wanderers were home and dry.
Wanderers boss Sam Allardyce recalled his captain Okocha to the starting line-up. It was the Nigerian's first start for three games because of a knee problem and the only change from the side beaten at Liverpool last week.
Fulham boss Chris Coleman decided to start with Brian McBride up front with Andy Cole. McBride came on a sub against Portsmouth last weekend and helped the Cottagers to three welcome points in the battle to stay out of the drop zone.
Otherwise, Fulham have not had much recent luck on the injury front with Papa Bouba Diop and Sylvain Legwinski two of their high profile casualties.
And the Londoners' fortune hardly improved when the game got underway, as former Wanderer Jensen was sent off in the 12th minute for deliberate handball on the line, with Okocha firing home the resulting penalty.
Yet Fulham only had themselves to blame for their misfortune. First Moritz Volz was careless enough to concede a corner, before Gary Speed's set-piece gave Bruno N'Gotty a free header, which was destined for the corner of the net until Jensen blocked it with his arm.
While Fulham seethed at their claim of injustice, Wanderers should have increased their lead as Nolan and Speed both wasted chances from good shooting positions. But the visitors' escape only proved temporary as Bolton added a second in the 33rd minute.
Okocha started the move with a deep cross from the left that Kevin Davies headed on into the path of Nolan, who beat Edwin van der Sar from close range for his fourth goal of the season.
And there could have been a third before half-time had Nolan and Stelios been a little sharper in the six-yard box, where they failed to control a low cross from Okocha.
After what was apparently a comfortable 45 minutes for the home side, they were knocked out of their stride in the opening two minutes of the second half when Fulham pulled a goal back.
The half started with Wanderers looking to repeat their early domination and Stelios saw his goalbound effort blocked by van der Sar. Yet a minute later it was Fulham who were celebrating.
Cole did well to hold play up on the edge of the area before releasing a pass to the far post where Boa Morte got in ahead of Nicky Hunt to slide the ball into the net.
Fulham's joy was short-lived, however, when Wanderers restored their two-goal advantage in the 54th minute when Nolan did well to set-up Stelios for his sixth goal of the season.
Yet despite that, Wanderers were not having things all their own way as Fulham continued to play Cole and McBride in attacking roles, which meant the home defence was never allowed much breathing space.
As the game wore on the fatigue element came into play and as the hard-working Fulham midfield began to tire, Okocha and Stelios were able to find extra space to start opening up the way to van der Sar's goal.
Okocha was also always looking for the chance to test the Dutch keeper but he was twice off-target with efforts from good positions.
Yet despite all that, Fulham always looked capable of catching Wanderers off-guard and Jussi Jaaskelainen was given a couple of uncomfortable moments.
One of those should have led to another Fulham goal when Volz set up a chance from down the right with a ball across the goalmouth that McBride was only inches away from putting into the net.
Fulham brought on Tomasz Radzinski and Collins John for Steed Malbranque and Cole for the final ten minutes, in the hope that fresh legs may just catch out Wanderers. And when Liam Rosenior fired in from the left, Jaaskelainen had to be alert to gather the ball as McBride hovered dangerously close by.
Wanderers followed suit with Ricardo Gardner and Khalilou Fadiga replacing Vincent Candela and Fernando Hierro, but Okocha was wasteful again when he fired a free-kick from a dangerous position straight into the defensive wall.
Yet it was Fulham who looked as if they were going to have the final word, John knocking the ball towards an empty net, only for Gardner to race back and clear off the line with an overhead kick.
After the game Fulham assistant boss Steve Keen said the club were considering appealing against Jensen's red card.
"Claus made a genuine attempt to chest the ball but obviously it caught his arm," claimed Keen. "We felt it was ball to hand rather than a deliberate hand ball.
"After that it was always going to be an uphill struggle but the boys never stopped working hard."
Allardyce said the result made up for last week's disappointment at Liverpool.
"We thought we should have got something from Anfield and it put some pressure on us for this game," he said. "But after the bit of luck with the penalty, we won with two quality goals."
Man of the Match: Kevin Nolan
Nolan did as much as anyone to ensure Wanderers clinched three vital points, scoring one and making another for the equally hard-working Stelios.