Almost straight from the kick-off, Rangers took the lead when Danny Shittu's mis-hit free-kick took a deflection to find Paul Furlong who turned sharply and fired inside Steve Simonsen's right post.
Stoke got to work quickly in search of the equaliser when, on ten minutes, Sam Bangoura set up Dave Brammer for a 20-yard volley but he scuffed his shot, sending the ball wildly over the bar.
Peter Sweeney's 26th minute free-kick gave Stoke the break they needed when his dangerous right-sided cross found the head of Bangoura who firmly finished into Simon Royce's bottom left corner.
City may have felt hard done by when, three minutes later, their shouts for a penalty were turned down when Bangoura was floored inside the area.
QPR capitalised on Stoke's brash temperament five minutes after the break. Simonsen parried a long shot but it was followed up by Furlong only for John Halls to prevent the striker from getting a shot in by bringing him to ground.
Richard Langley stepped up to take the spot-kick and slammed the ball past the helpless goalkeeper after 52 minutes.
The away side could have gone further ahead when former Port Vale winger Gareth Ainsworth had a shot deflected goalwards but Simonsen's quick reactions allowed him to tip the ball round his left post.
The Potters should have drew level again nine minutes from the end when man-of-the-match Luke Chadwick crossed for Mamady Sidibe but the forward put his free header well wide from only ten yards.
With the whistle blown for full-time, the tone was lowered when a fan from the home end seemingly jumped the barrier and attacked Royce before the pair were finally split up by several stewards.