Home goalkeeper Brian Jensen then produced two good saves to maintain Burnley's early lead, firstly when pushing a shot from Hugo Rodallega behind for a corner which then resulted in the goalkeeper producing a fine save to deny Mario Melchiot.
But there was a touch of farce about the Wigan equaliser as the Burnley defence were all at sea as Melchiot produced a ball to the far post, Jensen left his line, caught his studs in the turf and fell helplessly to the ground allowing Rodallega to tap the ball into an unguarded net. Moments later Jensen was replaced by Peruvian Diego Penny.
The game ultimately turned on a missed opportunity for the home side early in the second half when Chris Eagles could only fire into the side netting with goalkeeper Kirkland to beat.
That was to prove and expensive miss as striker Jason Scotland slid the ball into the path of Rodallega whose shot beat the diving Penny and went in off the far post.
The visitors made the game safe when Paul Scharner flicked on a corner at the near post for Emmerson Boyce to convert.
The nearest Burnley came to pulling a goal back was when central defender Clarke Carlisle headed against the top of the crossbar.
It's successive defeats for Owen Coyle's side and after their bright start to their first Premier League campaign, the ominous signs are that they face a long hard winter especially given the fact that they have yet to register a point away from Turf Moor.
For Roberto Martinez's team this win is confirmation that they have built on strong performances against Chelsea and Manchester City in recent weeks and on this form will pose a threat to any team in the division.