Fuller headed his fourth goal of the campaign as Rory Delap's long throws again caused mayhem at the Britannia Stadium.
And Stoke should have won by a wider margin as Sunderland, who beat fierce rivals Newcastle on Saturday, came back down to earth with a bump.
The visitors looked confident in the opening minutes and an early effort by Djibril Cisse was clutched by Thomas Sorensen at the foot of his near post.
But it wasn't long before Delap, playing against the club he left to join Stoke two years ago, caused serious problems with the first of numerous throws.
Mamady Sidibe headed on Delap's huge delivery and Anton Ferdinand did brilliantly to block Fuller's shot a yard from the line.
The attempt lifted Stoke and their fans and Phil Bardsley was happy to clear Seyi Olofinjana's cross for a corner, with the visitors defence now under the cosh.
Sunderland keeper Marton Fulop, a Stoke transfer target in the summer, then did well to beat out a 20-yard shot from Olofinjana as City continued to press.
Cisse headed a yard too high from Bardsley's 36th-minute cross, but Roy Keane's men were soon struggling to clear another Delap throw with Stoke still carrying the biggest threat.
And only an excellent piece of covering by Bardsley, after Sidibe had leapt above Danny Collins for what seemed the umpteenth time, halted Fuller's route to goal just before the break.
Keane replaced veteran Dwight Yorke with Kenwyne Jones at half-time, but Stoke were soon pushing again with Abdoulaye Faye almost getting on the end of a Tom Soares free-kick.
City went closer still just after the hour when Fuller created space to belt a shot which bounced off the face of Collins and rolled agonisingly wide of the far post, with Sidibe inches from making a decisive contact.
But Stoke's non-stop efforts finally brought their just rewards when Fuller broke the deadlock from yet another of Delap's throws in the 73rd minute.
Delap's delivery entered the danger area like a missile and Fuller got ahead of his marker to bury a firm header into the top right-hand corner of Fulop's net.
It should have been all over ten minutes from time when a super pass from Stoke substitute Michael Tonge released Fuller, who whipped a first-time shot against a post.
Sorensen, no more than a spectator for most of the night, was finally called into action in the 85th minute to claw out a decent effort from Jones, who had raced onto a pass from Kieran Richardson.
But a goal for Sunderland would have been daylight robbery at that stage and Stoke held firm to claim a richly deserved three points.