Wanderers were edged out on their own patch as Crystal Palace left the Reebok with all three points thanks to Glenn Murray’s second-half penalty.
Referee Geoff Eltringham awarded the visitors a 79th minute spot-kick after Palace teenager Wilfried Zaha went to the ground under a Zat Knight tackle, with Murray on hand to convert from 12 yards.
In a relatively even contest, Bolton’s best chance of the first half fell to skipper Kevin Davies, whose shot was blocked in a packed Palace penalty area, whilst several penalty appeals for Owen Coyle’s side were also controversially waved away.
Other opportunities also came the way of Mark Davies, David Ngog and, late-on, Chung-Young Lee but ultimately the ball just wouldn’t find its way into the Palace net.
Owen Coyle made one enforced change to the starting line-up that had won at Sheffield Wednesday, with loanee Stephen Warnock handed his debut in place of the injured Marcos Alonso.
It was Palace who carved the first chance of the game through the dangerous Zaha. The teenager found himself in space on the edge of the box and fired a low shot, but Adam Bogdan was up to the task and parried the ball out for a corner.
Bolton regrouped and enjoyed the majority of the early possession, with one noteworthy chance being a header from Ngog which flashed across goal and wide of the far post.
The Trotters continued to press, and the in-form Chris Eagles stepped up to bend a free-kick narrowly over the bar.
In the first 15 minutes Bolton were the best side and continued to enjoy the main share of possession with both Mears and Warnock getting forward to assist. But Palace were always dangerous on the break, with Zaha a constant threat.
Bogdan's second main contribution of the game was to deny Murray, who directed Owen Garvan's cross straight at the Hungarian.
Towards the end of the first half, Mark Davies’ had a legitimate shout for a penalty tuned down when he headed goalwards, only for the ball to strike the arm of Darcy Blake.
And shortly after, a goalmouth scramble saw both Eagles and Kevin Davies denied as Bolton continued to push forward.
However, Palace were inches away from going into the break with a lead when Murray’s second headed chance from eight yards missed the target by the narrowest of margins.
Bolton began the second half where they left off and Mark Davies was denied his second goal in as many games by a fine Speroni save. Good work from Eagles forced an opening for the midfielder, who brought the ball down, cut inside the Palace defence, only to see the Argentine keeper make a sprawling low stop.
The crowd was beginning to get behind the Wanderers, and it seemed to spur on the players. In the next attack, Eagles’ long free-kick was flicked on by Matt Mills and met by Kevin Davies, who couldn’t quite make enough contact to turn it past Speroni.
The game’s controversial moment followed ten minutes from time as Zaha weaved his way in the Bolton box and went down under the challenge of Knight. Referee Geoff Eltringham awarded the penalty to the frustration of the home crowd.
Glenn Murray stepped up to take the spot kick and made no mistake, firing the ball into the top corner.
Coyle made an immediate change, bringing off Eagles for Chung-Yong Lee who joined earlier substitutes Martin Petrov and Marvin Sordell.
As Bolton pushed forward for the leveller, Zaha continued to threaten, with the England Under-21 international flashing a cross-shot across goal
Late on, Chung-Yong went close with a long-range effort, but Palace would hold on to claim all three points to remain unbeaten through September.
Wanderers:Bogdan, Mears, Mills, Knight, Warnock, Andrews (Petrov 70), Spearing, Eagles (Lee 80), Mark Davies, Ngog (Sordell 76), Kevin Davies (Subs not used: Lonergan, Ream, Pratley, Ricketts)
Palace: Speroni, Ward, Parr (Moxey 64), Bolasie (Williams 75), Dikgacoi, Garvan, Blake, Jedinak, Zaha, Murray, Delaney (Subs not used: Price, Martin, Moritz, Goodwillie, Wilbrahim)