The Seasiders had led for the majority of the game following a goal from Jordan Rhodes in the opening stages, but were pegged back by a Josh Magennis equaliser in the closing stages of the game.
Well into stoppage time, Kenny Dougall was in the right place at the right time to give Neil Critchley’s side their first league win since the opening day.
The Tangerines opened the scoring after only four minutes.
CJ Hamilton’s cross into the box from the right side found Rhodes, who smashed the ball past Sam Tickle.
Jensen Weir came close to doubling the Seasiders lead, with his effort from the edge of the box forcing a good save from the Latics keeper.
Tickle also needed to be alert to stop a curling free kick from Callum Connolly.
The first real chance for Shaun Maloney’s side came just before the break, with a headed effort from a free kick landing on the roof of the net.
Following the restart, Weir forced Tickle into another save.
Jake Beesley did well in the build-up to lay the ball off to the Brighton loanee on the edge of the box.
Down the other end, Dan Grimshaw produced a fantastic stop to deny Callum Lang.
Wigan were able to eventually put the ball into the net, but the linesman’s flag was raised.
Meanwhile, Tickle was still being worked hard in the Latics goal, and was forced into a superb stop by Beesley.
With one minute of the 90 left, Latics levelled the scores, with a header from Magennis beating Grimshaw.
Despite the late setback, the Seasiders kept their heads up.
Well into stoppage time, Matty Virtue slotted a ball across the box for Dougall to smash into the back of the net.
Blackpool FC: Dan Grimshaw, Matthew Pennington, Olly Casey, James Husband, CJ Hamilton, Jensen Weir (64’), Ollie Norburn, Albie Morgan (81’), Callum Connolly, Jordan Rhodes, Jake Beesley (81’).
Substitutions: Rich O’Donnell, Marvin Ekpiteta, Matty Virtue (64’), Kenny Dougall (81’), Sonny Carey, Karamoko Dembele, Owen Dale (81’).