Town matched the FA Cup holders for long spells but paid the price for mistakes after Tommy Smith had given Blues the lead.
The New Zealand international volleyed in his fourth goal of the campaign but James McClean cancelled out the advantage within two minutes.
Poor defending from a free-kick just before half-time let in Leon Barnett to head home from close range and the Latics wrapped up the points 13 minutes from time with McClean rounding off a break after Town had lost the ball on halfway.
Jonny Williams came in for his home debut in the only change, with Sylvan Ebanks-Blake dropping to the bench.
Paul Anderson skimmed a header just over the bar from Stephen Hunt’s free-kick in the game’s first opening, then Luke Hyam won another free-kick on the edge of the Wigan box, Ali Al-Habsi holding on to Hunt’s delivery.
Jordi Gomez had Wigan’s first effort, his optimistic left foot drive from distance failing to trouble Dean Gerken.
Al-Habsi did enough to force Daryl Murphy’s shot from a Paul Anderson cross behind for a corner, then Anderson won a free-kick right on the edge of the box, Aaron Cresswell’s effort was blocked,
Cole Skuse headed the ball back into the danger zone and Smith hooked the ball into the net to give Blues a 19th minute lead.
The advantage lasted two minutes, Emmerson Boyce surged into the Town half before releasing Marc-Antoine Fortune and his cross was slammed into the net by McClean.
Cresswell and Williams linked up down the left but Barnett beat Murphy to the cross, then Williams almost found Hunt with a pass into the Latics’ box while at the other end former Town loanee Ryan Tunnicliffe saw his shot blocked by Luke Chambers.
McClean picked up the first yellow card of the 90 minutes for a foul on Williams, then Hyam blasted over from eight yards under pressure from Barnett.
Wigan went in front went in front four minutes before the break, Gomez sent in a free-kick and Barnett was left unmarked to head in from six yards to take the visitors into half-time ahead.
Town went close to levelling things up inside a minute of the second-half, Hunt crossed from the left after Williams had been denied in the box but Barnett beat everyone to the loose ball to clear the danger.
Murphy forced Ivan Ramis to concede a corner after the Republic of Ireland international latched on to the ball over the top but from the flag-kick, Wigan broke deep into Town’s half and at one stage had three on one, but Cresswell stayed cool to make a timely intervention as Fortune looked to strike.
Hunt and Ramis went into the book after a clash, then Hyam sent Anderson away with a terrific ball to force a corner but Barnett was there to prevent Murphy getting anything on the delivery.
Paul Green replaced Skuse in Town’s first change on the hour, Wigan responding with Martyn Waghorn making way for Nick Powell.
Green’s first involvement brought a yellow card for the midfielder for a foul on Gomez and from the free-kick, Barnett headed wide from a great position.
Paul Taylor was handed the last 20 minutes, replacing Anderson, the injured Barnett forced off with Rob Kiernan his replacement as both sides made their second change.
Blues were made to pay soon after though for losing the ball in midfield, Wigan broke through Gomez, who fed Fortune and from his cross McClean put daylight between the sides.
Sylvan Ebanks-Blake replaced Williams before the restart and saw his shot deflected over with his first touch, Al-Habsi then keeping out Taylor’s volley at the near post.
McClean made way for Stephen Crainey for the last 10 minutes as Wigan protected what they had to maintain their lead until the final whistle and secure an eighth successive win.