Stoke booked a rare place in the fourth round of the FA Cup after ending Wigan's recent run of nine consecutive wins while conceding only a single goal.
After going 16 games without a win, two goals from Chris Greenacre and a superb strike from Chris Iwelumo secured Stoke a third win in 10 days.
Wigan were on top in the opening minutes but had nothing to show for their efforts as Stoke defended well giving little away at the back.
John Filan managed to hold on to a 15-yard shot from Brynjar Gunnarsson at the second attempt, then beat out a shot from Bjarni Gudjonsson as Stoke hit back.
The home side went in front in the 20th minute after Greenacre had won a corner on the Wigan right.
The visitors only half cleared and James O'Connor slipped the ball back into the box to Greenacre who sent in an angled shot from the corner of the six-yard box.
Greenacre almost added a second, firing into the side netting following a delightful pull back by Stokes Dutch winger Peter Hoekstra.
The home side were not having it all their own way, but in the 31st minute they increased their lead with a goal worthy of winning any game.
O'Connor sent Hoekstra away on the left and his cross was met by Iwelumo who crashed a ferocious 15-yard volley into the net before Filan could blink.
Greenacre secured the win midway through the second half, meeting Marcus Hall's left wing cross with a glancing header to send the ball inside the far post.
A delighted Greenacre said, "It was a great ball in and I just managed to get in front of the keeper and score. I am chuffed to bits and I can relax tonight and look back on a good days work."