Wolves took an early lead through Matt Jarvis, who curled an effort into the top corner, but their lead lasted barely three minutes.
Franco Di Santo levelled with a low finish before Emerson Boyce put Wigan ahead two minutes later with a thumping header.
Boyce scored a brilliant dipping volley to put daylight between the sides before Stephen Fletcher tapped in a late consolation for Wolves.
Following their eye-catching wins over Liverpool, Manchester United and Arsenal, Wigan have secured their Premier League status for an eighth season.
But, somewhat ironically, Wigan found themselves behind when the home fans were applauding throughout the eighth minute of the game, to celebrate the feat.
The Wigan defence allowed Jarvis too much space on the edge of the box, and the winger curled a beautiful effort into the top corner.
But Wolves’ lead lasted barely three minutes. Stephen Hunt was dispossessed and, with Wolves unable to clear the loose ball, Di Santo fired into the bottom corner.
With Wolves on the ropes Wigan struck again through Boyce, who met Jean Beausejour's corner with an emphatic header.
Wigan dominated and chances for Di Santo and Shaun Maloney went begging in the second half.
But Wigan eventually extended their lead through Boyce, who beat Jan De Vries with an explosive dipping volley from distance.
Wolves salvaged some consolation with Fletcher's late tap-in after Kevin Doyle had caused chaos in the Wigan box, but it could not prevent Terry Connor's side ending their Premier League campaign in miserable fashion.