Lee McCulloch netted an 87th minute cracker to maintain Wigan's unbeaten record and their six-point lead at the top of the Championship.
A hard-fought contest looked to be heading for a stalemate, before David Graham instigated a swift raid which led to McCulloch's fifth goal of the campaign.
Alan Mahon was also involved before McCulloch latched on to a 25-yard half-volley, sending his shot just inside the helpless Ed de Goey's left-hand post.
Stoke made a barnstorming start with Chris Greenacre warming John Filan's fingertips with an acrobatic volley from a Wayne Thomas cross.
And Filan then plunged to his right to pull off a brilliant one-handed save from Darel Russell's close-range strike in the tenth minute.
But Wigan gradually settled into their stride and squandered several opportunities to take a half-time advantage.
The elusive Nathan Ellington clattered a close-range shot over the top in the melee which followed Jimmy Bullard's 37th minute corner.
And McCulloch wasted a glorious opportunity three minutes later when he fired way off beam with the goal at his mercy after excellent work by Ellington.
Chances were more infrequent in the second period, but Wigan certainly bossed possession and came within inches of taking a 63rd minute lead.
Mahon only half-hit his shot from a Leighton Baines cross and it was like a slow motion replay as the ball struck de Goey's right-hand post.
But McCulloch atoned for his earlier miss to leave the joyous Wigan contingent chanting: "We are unbeatable".