Ryan Shawcross opened the scoring for Stoke and the game looked over when Peter Crouch added a second after the break but goals from James McArthur and Franco Di Santo earned Wigan a point.
The Latics deserved their rewards for a high-tempo second half display but Roberto Martinez will surely be alarmed by the defending that saw his side go behind.
Jean Beausejour could only head his attempted clearance from a free-kick against team-mate James McCarthy and the ball looped over both men to allow Shawcross to volley home from close range.
That breakthrough came midway through the first half and was befitting of the scrappy start to the game.
But it was Stoke applying the bulk of the pressure early on with Charlie Adam going close to doubling the lead shortly afterwards with a rare right-footed effort from distance.
And it was a driving run from Adam that led to Stoke's second goal in the early stages of the second half.
The Scot broke and was given freedom to get a shot off from the edge of the box that Ali Al-Habsi could only parry into the path off the advancing Crouch who tucked the ball away.
Just as the home fans were expecting a comfortable evening, Wigan scored the goal of the night - Roger Espinoza threading a pass through to McArthur who finished expertly with the outside of his boot.
Espinoza was fast becoming the pivotal figure with his passes finally finding their range and the Honduran combined with McArthur again to help haul the visitors level.
He curled in an angled ball from the left that McArthur headed back across goal for Di Santo to volley cleanly past Asmir Begovic and earn Wigan an unlikely equaliser.
Cameron Jerome came off the bench to fire wide but neither side could find a fifth goal and the point is enough to move Wigan out of the drop zone and above Aston Villa and Reading into 17th spot.