Goals from strike duo Ricardo Fuller and James Beattie in a thrilling second half proved the difference as the hosts clinched their 10th win on home soil.
It was also 10 for Fuller, who teased the Latics' defence before reaching double figures in his league goals tally.
Steve Bruce's side, who have now failed to win in 15 of their last 17, had chances and dominated in spells but the Potters secured the win when Beattie headed in from a brave assist by Matt Etherington.
Goal-shy LaticsPart of the reason for the Latics' terrible run is their inability to score, with just nine league goals since the start of the year, and the problem reared its head again.
The Latics had the better of the first half but could not take their chances, whereas in Fuller and especially Beattie, Stoke have strikers who score important goals.
Wigan carved out their first chance less than two minutes in when Hugo Rodallega headed a long punt forward into the path of Paul Scharner but his angled drive was straight at Thomas Sorensen.
Debutant Cho Won-hee's 13th-minute through-ball sent Scharner running into the penalty area but although the Austrian went down in a tussle with Abdoulaye Faye referee Lee Probert waved play on.
Stoke's first shooting opportunity fell to Glenn Whelan moments later but he screwed a long-range effort well wide.
Super saveCho, who had enjoyed a gentle introduction, forced Sorensen to tip over his 19th-minute 30-yard shot at full stretch but the Korean's second effort from the resulting corner was embarrassingly high.
Rodallega, after scoring in his last two matches, was next to try his luck from distance but he too was well off target.
Nothing was going right for either side; exemplified when one of Rory Delap's trademark long throws ended up in the back of the net without anyone getting a touch on it just after the half hour.
Faye's back-header from Richard Kingson's long kick sent Rodallega clear but his shot from the right of the area rolled harmlessly across the face of goal.
Untidy play was evident at the other end too as Fuller's poor touch in the penalty area took Beattie's low cross away from the onrushing Liam Lawrence.
There was no change in the level of quality unfortunately as within six minutes of the restart Lee Cattermole mis-controlled Charles N'Zogbia's left-wing cross inside the six-yard area when it looked easier to score.
N'Zogbia was not exempt from criticism either. First he was guilty of wastefully crossing too near Sorensen after Rodallega had dispossessed Danny Pugh to set up a counter-attack.
The French winger then blazed over having run 30 yards with the ball after Wilkinson's slip on the halfway line.
Cho was replaced by Ben Watson in the 58th minute, just before substitute Pugh's swerving half-volley from a partially-cleared corner flew inches over the crossbar and Wigan left-back Maynor Figueroa drilled a left-footed shot narrowly wide.
BreakthroughWhen the breakthrough came in the 69th minute it was largely thanks to Fuller's persistence and Wigan's inability to clear their lines.
There appeared to be little danger when Lawrence played a high ball up to the striker, closely watched by three defenders.
Emmerson Boyce, Titus Bramble and Figueroa all had chances to tackle Fuller but he battled on and somehow had enough time to pick a spot high to Kingson's right.
Mido was sent on for midfielder Michael Brown as Steve Bruce reverted to 4-4-2 but before they had time to reorganise Wigan were 2-0 down in the 76th minute.
Delap's ball inside Mario Melchiot released Etherington down the left and as Kingson raced out he scooped a cross to the far post where Beattie headed home.
With the match won the game reverted to type but that did not bother the home faithful one bit as they are already looking forward to a second successive season in the top flight.
1st Half Goals
Shots on Target
Shots off Target