Johan Elmander's fifth goal of the season ensured Wanderers extended their unbeaten run to five games in the league.
The Swede reacted quicker than anyone to pounce on a loose ball inside the Wigan area after a flick on from skipper Kevin Davies to level the scores midway through the second period.
Wanderers had impressed, especially in the opening 45, but in the second half Hugo Rodallega opened the scoring firing past Jussi Jaaskelainen having latched onto a through ball.
But Owen Coyle's men continued to probe and got their reward just after the hour mark, when Elmander sent the travelling fans wild after converting from point blank range.
Manager Coyle stuck to the same starting XI that successfully took three points off Stoke City last weekend.
The only change for Wanderers was on the bench, where Tamir Cohen replaced the suspended Ivan Klasnic.
With Ali Al-Habsi ineligible to play against his parent club, Chris Kirkland started the game between the posts for Wigan.
The Trotters were out to maintain an impressive run of form that has seen them lose just one of their opening eight Barclays Premier League games, and started positively.
A sustained period of possession in the opening minutes of the game culminated in Davies stooping to head narrowly over the crossbar from Martin Petrov's dangerous cross from the left flank.
Petrov continued to cause problems for the hosts. Ten minutes in, the Bulgarian cleverly won a free-kick on the left touchline, which he fired into the box, with the ball falling at the feet of Gretar Steinsson who saw a looping cross-cum-shot land on the roof of the net.
Moments later Wanderers mustered a half chance after a fantastic flowing move. Petrov's sublime diagonal ball picked out Chung-Yong Lee, and after nice interplay between the Korean, Fabrice Muamba and Steinsson, Davies saw a volley sail narrowly over the crossbar.
Wigan's only attempt of note in the early throes of the game came from Charles N'Zogbia. The Frenchman fizzed a dangerous free-kick into Bolton box which Jaaskelainen did well to claim.
Petrov fired over from distance, as Wanderers continued to probe. Testament to how well the side had started the game was clear to see, as the home fans began to voice their concerns.
And the home side suddenly sprung into life. Colombian Rodallega darted across the Wanderers box before feeding N'Zogbia, who then saw a curling effort drift narrowly wide.
Rodallega then latched onto a through ball but was denied by a sprawling Jaaskalainen and moments later the Wanderers stopper thwarted the same player after a penetrating run, as the hosts began to get a foothold in the game.
After the break Rodallega continued to look lively, pouncing on a loose ball inside the Wanderers area and curling an effort narrowly wide.
The second period has started in a much more frantic fashion, as the volumes levels rose from both sets of supporters.
And on the hour mark the deadlock was broken by Rodallega, who had looked the only real source of danger for the home side, latching onto a through ball before calmly finishing low beyond Jaaskelainen.
Buoyed by their opener, Wigan continued to press. Ex-Chelsea man Franco Di Santo saw an effort from the edge of the area drift wide.
Coyle shuffled his pack with a double substitution, introducing on-loan Benfica man Rodrigo for his Premier League debut and Matt Taylor.
And that move soon paid off as Wanderers levelled the scores through Swede Elmander.
Wigan failed to deal with a looping ball into the area, and Davies nodded down into the path of Taylor, who did fantastically well to keep the ball alive before Elmander reacted quicker than anyone to prod home from inside the six yard box and send the travelling contingent wild.
Rodrigo was looking impressive and his confidence levels were clearly sky-high, as he attempted a spectacular volley following a crossfield pass from Taylor which worked goalkeeper Kirkland.
Wanderers enjoyed large spells of possession, but the hosts did look dangerous and a superb tackle from Paul Robinson denied N'Zogbia a clear goalscoring opportunity, as game moved into the final 15 minutes.
Rodallega again came close, this time with a back post header from a corner that flew across the face of goal.
Rodrigo came close to winning all three points for Wanderers with a back post effort from Stuart Holden's cross, but there was to be no further goalmouth action, as the referee called time on proceedings.
Wigan Athletic: Kirkland, Alcaraz, McCarthy (Diame 30), Thomas, Di Santo, N'Zogbia, Caldwell, Gomez (Cleverley 83), Boyce (Stam 52), Rodallega, Figueroa (Unused substitutes: Nicholls, Watson, Boselli, Moses)
Wanderers: Jaaskelainen, Steinsson, Cahill, Knight, Robinson, Chung-Yong (Rodrigo 65), Muamba (Davies 86), Holden, Petrov (Taylor 65), Davies, Elmander (Unused substitutes: Bogdan, Ricketts, Blake, Cohen)