Antolin Alcaraz's late goal relegated Blackburn from the Barclays Premier League and ensured Wigan's safety in a nervy game at Ewood Park.
Only a win would have saved Steve Kean's side from relegation, but Alcaraz's 87th-minute header proved to be the only goal and condemned them to npower Championship football next season.
Blackburn had earlier seen a penalty chance turned down by referee Mark Clattenburg when Junior Hoilett was brought down by Emmerson Boyce in an error-strewn performance by both sides.
Rovers supporters, perhaps already resigned to their fate, had turned the game into one long protest against manager Steve Kean and owners Venky's and several invaded the pitch at the final whistle.
A live chicken had even been released early in the game, presumably in protest against Indian poultry giants Venky's, whose takeover in 2010 is pinpointed by many as the start of the club's demise.
On a worrying note, Gael Givet, who has a heart condition, left the action at half-time amid rumours of further problems but he was seen soon after taking a seat in the stand.
What action there was saw Wigan do the early attacking with Franco di Santo bursting clear only to shoot straight at Paul Robinson.
For Blackburn, Hoilett blasted over and then briefly excited with a mazy run before shooting tamely at Ali Al Habsi.
As the second half began, a Rovers fan ran across the pitch waving his season ticket in the air. It was a curious protest because when he reached the dugout he showed it to Wigan boss Roberto Martinez, rather than anyone connected to his own club.
The winner came from a corner as time ran out. Alcaraz timed his leap superbly to meet Jean Beausejour's deep cross and powered a header goalwards which Robinson, despite a valiant effort, could not palm out.