Hugo Rodallega's two goals helped end Burnley's 100 per cent record at Turf Moor since stepping up to the Barclays Premier League.
The Colombia striker has now scored five goals this season, with all four of Wigan's wins coming when he has been on the scoresheet.
After cancelling out Steven Fletcher's fourth-minute opener just 11 minutes later, Rodallega added his second early after the restart.
That was before a rare Emmerson Boyce strike assured Wigan a first away win since the opening day of the campaign.
Burnley were a shadow of the energetic team that had caused such a stir after victories over Manchester United, Everton, Sunderland and Birmingham City on this ground, as they lacked momentum and ideas.
That is taking nothing away from Wigan, who could not have started the match more disastrously as Burnley seemed set to add the scalp of their local rivals to their list of conquests so far.
low cross
It was a simple goal, with the industrious Robbie Blake carving out space on the left before curling in a low cross to the far post.
Sliding in, Fletcher flicked the ball up, and for a moment perhaps thought he had missed a sitter from just two yards out.
The ball, though, struck the underside of the crossbar, dropping on the line before its momentum carried it into the net to give Owen Coyle's side the perfect start.
Despite that, goalkeeper Chris Kirkland, having recovered from a dislocated finger sustained in last Sunday's 1-1 draw at home to Manchester City, had nothing to do for the remainder of the half.
Instead, Wigan, clearly stung into life, were back on level terms seven minutes later, and that after two superb saves from Clarets goalkeeper Brian Jensen.
Initially, Jensen turned aside a rasping right-foot drive from 18 yards from Rodallega in the ninth minute.
own area
From the ensuing corner, whipped into the far post by the Colombia striker, captain Mario Melchiot was denied by Jensen's reactions as he blocked on the line the defender's point-blank shot.
Two minutes later, though, Jensen was an embarrassed figure as he slipped inside his own area, his foot caught in the turf, as he came to collect an innocuous Melchiot cross, giving Rodallega a simple tap-in from eight yards.
There was arguably a degree of wounded pride etched on the face of Jensen, along with the pain he was clearly in, as he had sustained an injury in the process.
Despite lengthy treatment, Jensen limped off four minutes later to be replaced by Peru international Diego Penny, on for his Barclays Premier League debut.
Penny was a spectator until six minutes after the restart when he was picking the ball out of his net as Rodallega scored his and Wigan's second.
Two minutes after Burnley's Chris Eagles had hit the side-netting, Jason Scotland set up Rodallega.
late onslaught
Collecting the ball inside the area, Scotland played a simple pass back to Rodallega who unleashed an 18-yard right-foot drive that beat Penny in off his left-hand post.
Even after that Burnley failed to rouse themselves, flickering into life either side of David Nugent's arrival in the 67th minute for Blake.
Kirkland, for so long an onlooker, initially held onto a low shot from Andre Bikey before then denying Graham Alexander with a low save down to his right.
That should have been the cue for a late onslaught, instead it was Wigan who went on to seal the three points in the 76th minute.
From a Rodallega corner flicked on at the near post by Paul Scharner, no Burnley player picked up Boyce who sidefooted home only the second goal of his Latics career, with his first coming 11 months ago.
The home side came close to pulling one back when Clarke Carlisle looped a header onto the bar soon after, but that was as close as they came to stealing anything from a match deservedly won by Wigan.
