Kenwyne Jones and David Healy were the Black Cats' heroes as they broke City hearts late on.
The victory was no less than the Wearsiders deserved having they fought hard all afternoon to break down a resilient City rearguard.
Ricky Sbragia's side had laid siege to the City goal for long periods, but were unable to find the breakthrough until Jones weighed in with his ninth goal of the campaign.
At times Stoke had nine or ten men back as they tried to hold out, but it was all in vain in the 79th minute.
Andy Reid swung in a cross from the left and Jones got just enough on his back-post header to nod it past Tommy Sorensen in the Stoke goal.
An audible sigh of relief followed the cheers of the home fans, who must have thought they were going to suffer from another bout of ref justice.
The Sunderland supporters had seen their side robbed of three points in the Tyne-Wear derby less than seven days earlier when Howard Webb awarded a penalty which never was.
Today referee Rob Styles refused to give what was a clear spot-kick in the 40th minute. Reid got to the byline and lobbed a ball to the back post where Steed Malbranque stooped to head home.
Stoke substitute Danny Pugh had other ideas and swung his arm at the ball to prevent a certain goal.
Neither Styles nor his assistant, who seemed well placed, saw the deliberate foul and despite the Wearsiders' protests waived away their appeals for a penalty.
The hosts should have been ahead before then as Jones forced a great save from Sorensen with just seven minutes played - the Trinidad & Tobago striker firing in a powerful drive from just inside the area.
Three minutes later the visitors went close as Richard Cresswell's overhead kick from inside the 18-yad box drifted just wide of the target.
Having struggled for points on their travels this was never going to be an easy afternoon, for the Potters.
Of course, the visitors posed their usual aerial threat early on, but their gameplan went out of the window in an injury-plagued first half.
The Potters had to make all three of the substitutions in the opening period - three times in the space of 13 minutes City boss Tony Pulis had to make a change as first Andy Wilkinson, then Ryan Shawcross and Ricardo Fuller had to be replaced before the half-hour mark.
That obviously had an effect on Stoke and Sunderland bossed proceedings for the remainder of the encounter and they went close again right on half-time.
Reid's cross was met by Djibril Cisse and the Frenchman's header was cleared off the line by Stephen Kelly.
The hosts continued to pressure City after the break and Sorensen was forced to make a good save with his legs just two minutes into the second half.
If the spate of injuries had left Stoke with a hill to climb, that became a mountain on 66 minutes as Matthew Etherington received his marching orders. It was yet another strange decision from Styles.
Danny Collins blocked Etherington from the ball and Stoke man flicked out a kick. The City player was shown a straight red which seemed ridiculous, while Collins was booked and the visitors were awarded a free-kick.
It was from this set-piece that the away side had their best chance. The ball was played in and a good block from Phil Bardsley saw it drop to new signing Henri Camara, who somehow managed to hit the crossbar from a yard out.
It was Stoke's only real chance and once the Wearsiders went one up there was no looking back.
Healy made sure in the final minute, netting with virtually the last kick of the game.
Kieran Richardson fed Jones on the edge of the area and the big striker turned his man before sliding a ball across the face of the goal.
Healy was in just the right position to fire home and seal a deserved win.