Craig Davies condemned Huddersfield Town to a third straight away defeat and earned Bolton's fourth win in as many home games under Neil Lennon with a second-half strike.
Chris Powell's side produced a battling display, but their hopes of keeping a second successive clean sheet and hitting on the counter-attack were shattered.
Town made three changes for the Lancastrian clash, recalling keeper Alex Smithies, left-back Jack Robinson and striker Nahki Wells.
Joe Murphy, who kept a clean sheet against Sheffield Wednesday the week before but was ruled out by a foot injury, Paul Dixon, who was in the bench, and Harry Bunn (thigh) missed out.
Bolton, unbeaten in their three previous games, were unchanged as they sought the win which would move them further away from the Championship danger zone.
The home side had the first clear chance 10 minutes in when frontman Davies crashed a shot against the bar.
The Welshman also had a curling long-range effort held by Smithies before Bolton had a penalty appeal turned down, Mark Hudson's foul on Davies being ruled outside the area.
Town skipper Hudson received a yellow card while Liam Feeney was off target with the free-kick before Diego Poyet made a vital block to thwart Lee Chung-Yong.
Town's best chance of the half came in time added in when Jacob Butterfield picked out Wells, whose shot was pushed wide by Andy Lonergan.
Town had a great chance to snatch the lead three minutes into the second half, but Jacob Butterfield's close-range shot from Scannell's cross was saved.
Butterfield then set up Grant Holt, who beat keeper Lonergan in a 50:50, but poked the ball just wide.
Bolton finally made the breakthrough in the 67th minute, pouncing on a slip by substitute Murray Wallace, with Davies drilling home from Feeney's cross.
Town also had Wallace booked, while Bolton's Lee and Neil Danns were cautioned.
