Lee McCulloch's goal gave Wigan their third consecutive win and inflicted a second home defeat in a week on Bolton.
Bolton's Anelka and Wigan's Boyce tussle for the ball
A dour first half saw few chances and little entertainment, but the second period was much more worthy of a derby.
And with 11 minutes left, McCulloch fired home with his right foot from 18 yards after a clever Wigan build-up.
Stelios Giannakopoulos did put the ball in the net for Bolton at the end of the first half but El-Hadji Diouf had already been ruled offside.
Bolton's home has been a notoriously difficult place to visit this season but the Trotters were also beaten by Manchester United last week.
But Wigan's fortunes are on the rise after a difficult start to the season and they have now kept three clean sheets in a row.
The last time Wigan won away at Bolton was in the old Division Three, and the first-half fare was more lower league than Premiership standard as both sides struggled to penetrate.
Anelka was put clean through by Diouf after 11 minutes but blazed his shot over.
Overestimating the height of the target was a recurring theme, with Diouf and Wigan's David Cotterill among those also blasting over decent chances.
Wigan boss Paul Jewell did have some excuse for the disjointed display in that he had to shuffle his pack in the first half when Emile Heskey and then Gary Teale were injured inside 33 minutes.
There was additional anxiety for Jewell when Chris Kirkland felt the forearm of Kevin Davies in a challenge for a high ball.
The injury-prone Wigan goalkeeper required treatment but groggily got to his feet.
Much of the crowd were probably also in a stupor after a numbing first half, but a frantic melee in the Wigan goalmouth in the opening minutes after the break set the tone for a more entertaining second period.
A much more open game threw up many more chances and the crowd at the Reebok did their best to stoke up the derby atmosphere.
Davies glanced a header just wide from Ivan Campo's corner, and Arjan De Zeeuw did well to poke the ball away at full stretch from an advancing Diouf.
Wigan were also showing more purpose about getting into their opponents' penalty area.
Henri Camara twisted his way through the Bolton defence before running out of steam while sub McCulloch posed more threat than Heskey, the man he replaced.
Bolton had the better of the first half of the second period but Wigan began to look more dangerous and broke the deadlock after 79 minutes.
Some clever quick passing from Kevin Kilbane and Camara released McCulloch, who lashed home from just outside the box.
Cotterill could have doubled Wigan's lead in the dying minutes but Jussi Jaaskelainen did well to keep out his fierce right-footed shot from 20 yards.
Bolton continued to search for the equaliser and Abdoulaye Faye nodded just wide in injury time as Wigan desperately defended their lead.
Wanderers stay fourth in what remains their best-ever start to the Premiership.
But manager Sam Allardyce was left to mull over five goals conceded without replay at the fortress Reebok in the last two games.
Bolton manager Sam Allardyce:
"Nic has not produced the sort of quality we know he has in abundance.
"We have to be patient, though, we cannot put that much pressure on him. We have 11 players in the side after all.
"He is OK. We just have to use him more and get more ball to him.
"I will stick with him, he has electrifying pace and when he gets behind defenders nobody can catch him. He can provide a goal as well as score a goal.
Wigan manager Paul Jewell:
"It was never going to be a great match but as a defensive unit it was a great display by my side.
"We have worked exceptionally hard on the back four since the Manchester United game (which they lost 3-1).
"We had become a bit brittle but we have got that steely determination back."
Bolton: Jaaskelainen, Ben Haim, Meite, Faye, Pedersen (Hunt 90), Giannakopoulos, Campo, Speed (Tal 90), Davies (Vaz Te 74), Anelka, Diouf.
Subs Not Used: Al Habsi, Smith.
Wigan: Kirkland, Boyce, Webster, De Zeeuw, Baines, Teale (Cotterill 33), Landzaat, Scharner, Kilbane, Heskey (McCulloch 28), Camara (Johansson 88).
Subs Not Used: Filan, Jackson.
Booked: Kilbane, Landzaat.
Goals: McCulloch 79.
Ref: M Clattenburg (Co Durham).