The Potters returned from Sunderland pointless but with yet another major refereeing decisiong going against them.
Asamoah Gyan's double won the points for Sunderland whilst the main controversy saw a blatant double handball on the line from Lee Cattermole, denying Jones an equaliser with plenty of time left for City to make a what should have been 10 men Sunderland pay.
After a bright start by Stoke the deadlock was broken by the hosts as Gyan tapped in from close range after Begovic had done well to save Welbeck's initial shot.
After both sides traded chances, Tuncay and Jones both going close for Stoke whilst Malbranque and Gyan both forced Begovic into smart stops, Sunderland missed a golden opportunity to double their advantage when they were awarded a spot kick following Walters foul on Welbeck. Malbranque stepped up but Begovic was equal to it and pushed his effort away to safety.
The second half started with both sides pushing for the games secong goal but wayward finishing and brave defending denied Etherington, Tuncay and Huth for Stoke and Gyan and Welbeck for the hosts.
City looked to have got themselves level on 70 minutes when Etherington's corner was headed goalwards by Jones, the strikers effort blocked with the ball two-thirds over the line by the arm of Cattermole. Cattermole then preceded to push his arm up to handball the ball a second time and push the ball away from goal. The Potters should have been awarded a penalty, and Cattermole a red card, but the ref, who seemed to have a perfect view, just waved play on.
The sense of injustice surrounding the club has been building in recent weeks and it seemed to get too much forcaptain Ryan Shawcross, as he collected two yellow cards to get sent off with ten minutes left.
All that was left was for a second Black Cats goal as Gyan ran through to smash an effort past a helpless Begovic and guarantee the points.