The result also put Wigan six points clear of their neighbours after an incident-packed nail-biter at the JJB Stadium.
The Latics had got off to a disastrous start when Wales midfielder Jason Koumas was controversially sent off after five minutes.
Referee Steve Tanner had no hesitation in reaching for the red card after deciding the challenge which left Gary Cahill on the deck but uninjured fell into the dangerous category.
It did look harsh on the ex-West Brom star and it was tough on the Latics so early in the action.
But Wigan still produced the best early chances as Heskey steered a header wide from Antonio Valencia's cross and Wilson Palacios had a screamer from the edge of the box deflected for a corner.
El Hadji Diouf came up with Bolton's first threat by glancing a header just wide as both sides opted for a direct, no-nonsense approach in blustery conditions.
Wigan appealed in vain when Ivan Campo cleared a Paul Scharner header off the line with the Austrian defender insisting it had gone in.
But the sense of injustice was instantly forgotten when England striker Heskey latched onto a long throw in from Valencia to lash his shot past Ali Al-Habsi from six yards to give Wigan the advantage.
It was only Heskey's goal second of an injury-hit season and his first since the game at Sunderland way back in August.
Predictably it sparked Bolton into action and they were denied an equaliser when Diouf beat Chris Kirkland from close range, but the effort was ruled out by the referee.
Wanderers lost Tamir Cohen after a clash of heads with Erik Edman, but substitute Grzegorz Rasiak went close to levelling it up after forcing an excellent save from Kirkland with a diving header.
A clash between Michael Brown and Campo threatened to turn ugly and the pair had to be kept apart as they left the pitch at half-time.
Kirkland proved his quality as he twice came to the rescue early in the second half with saves from Matthew Taylor and Kevin Nolan, while Scharner almost put through his own goal as Bolton piled on the pressure.
Andy O'Brien was almost left red-faced when he headed over his own keeper but luckily got away with conceding only a corner.
Bolton were furious after claiming in vain that Brown handled on the line from Kevin Davies and Wigan were forced to hang on desperately during four minutes of added time.