All the goals came in the first half, with Robert Huth getting the ball rolling with an 18th-minute free-kick that deflected in off Mohamed Diame in the wall.
If the Latics were cursing their luck, they got some of their own half an hour in as Danny Collins diverted Ben Watson's free-kick past his own goalkeeper.
Parity lasted less than two minutes as Stoke broke down the right, where Kenwyne Jones and Fuller combined to tee up Matthew Etherington, who finished well.
The Latics were somewhat unfortunate to fall behind.
But five minutes before the break, the home fans were celebrating, and for the third time a deflection played a crucial part in a goal. Tom Cleverley cut in from the right and let fly from 20 yards, with the ball taking a key touch off Rory Delap and nestling in the corner.
Source: PA
Source: PA