It took a two goal deficit for Latics to kick into gear after they fell behind to a Ryan Shawcross volley and Peter Crouch tap in but, James McArthur bit back with a right footed one-on-one and Franco Di Santo equalised after some incredible build-up
Latics dominated from their equaliser to the last minute as they teased Stoke and riled the crowd with constant possessional pressure.
Roberto Martinez made eight changes from the side that beat Macclesfield Town in the FA Cup fourth round but the big news was that Roman Golobart kept his starting place and was handed his Barclays Premier League debut.
It was a back and forth start to the game in terms of possession as Latics put their passing style of football to the test against Stoke's long ball directive.
The game was stopped four three minutes when a hanging ball in the Potteries wind resulted in a bloody clash of heads between Robert Huth and Franco Di Santo.
Both received treatment and had their wounds strapped up to ensure they could play on.
For the opening 20 minutes the hosts were held off by the towering figures of Roman Golobart and Gary Caldwell and apart from long range efforts from Jon Walters and Charlie Adam fizzing wide they didn't pose a sufficient threat.
On 23 minutes though, one of those balls into the box paid off with a huge slice of luck as Charlie Adam's left footed ball into the box from a free kick on the right wing was headed by Jean Beausejour onto the back of James McCarthy's head and into the path of Stoke captain Ryan Shawcross who volleyed in from close range.
The goal unsettled Latics' rhythm momentarily but as the half grew on Latics did so too with the best chance falling to James McArthur from close range after Beausejour beat Geoff Cameron down the left and lashed the ball across the box.
McArthur came in quickly side footed but the power on the ball caught him out as his effort went wide.
The second half didn't start as planned and Stoke doubled their lead with Peter Crouch sniffing a chance as Charlie Adam's long range effort was parried into the path of the England international by Ali Al Habsi.
Roger Espinoza had been fouled in the build-up but nothing was done as Stoke looked to take control.
Moments later though Latics gave themselves a fighting chance with the simplest of goals.
James McCarthy played the ball from just inside his own half to Franco Di Santo who came deep, the Argentinian laid the ball off to the outstanding Espinoza who threaded it between the Stoke defence and into the path of McArthur as he fired it in with the outside of his right foot and in off the post.
Latics could sense the fear in the Stoke side and the anguish in their supporters and continued a constant barrage of attacks.
Ten minutes after the first goal Latics got their second with another superb move.
Espinoza played his part again as he curled in a cross from the left edge of the area, McArthur nodded it down into the centre of the area and Di Santo beat his man to rifle Latics level with his right foot.
More and more possession was given to Latics and at some stages they were putting moves of 20 to 25 passes together.
Roots to the goal were well blocked by Stoke until the 89th minute when a cute Maloney cross from the right beat the defence but an outstretched leg from Di Santo didn't provide enough contact, if it had it would surely have been in.
Stoke only real chance of the second half fell to Charlie Adam who almost got a clear shot on goal from close range but found the brick wall of Roman Golobart who made a goal saving tackle on his debut.
Latics impressive performance in the second half will carry great momentum into the weekend as they gear up for the clash with Southampton.