Gareth Ainsworth will be rueing the penalty he missed with the home side in cruise control for most of the first half, but Stoke proved to be the more clinical of the sides in the end.
QPR started well and Lee Cook forced Stoke keeper Steve Simonsen to tip over the bar in the first minute.
It did not take long before the early pressure eventually told for the home side, and it was Danish striker Marc Nygaard who opened the scoring on seven minutes with his seventh goal of the season.
A long Steve Lomas throw resulted in a goalmouth scramble, in which Sammy Youssouf had a shot blocked, but Nygaard made no mistake as his well-hit shot squirmed under Simonsen.
With a goal in the bag, the home side played some patient football, with Stoke rarely launching a meaningful attack.
The frustration of having to do most of the running must have got to City midfielder Dave Brammer on 24 minutes, and to concede a penalty with Cook going nowhere was absolute madness.
Luckily for him, Ainsworth was unusually wasteful from the spot, and his poor penalty was easily smothered by Simonsen.
This gave Stoke the confidence they needed to get forward, and they nearly made QPR pay when Peter Sweeney played in Hans Sigurdsson who should have finished better.
He hit his shot straight into the body of home keeper Paul Jones, but Luke Chadwick was a little unlucky to see his header bounce onto the bar on the rebound.
Although QPR again started the second half brighter with Ainsworth forcing a save from Simonsen on 50 minutes, they then allowed Stoke to have a period of dominance which they finally took advantage of.
The introduction of top goalscorer Paul Gallagher had an immediate impact, as he played in Darel Russell on 72 minutes who went over a Dan Shittu challenge in the box for a penalty.
Carl Hoefkens showed Ainsworth how to deal with the pressure, and he made no mistake in sending Jones the wrong way.
Stoke then saw the opportunity to then take all three points and duly did.
After forcing a double save out of Jones on 79 minutes, Sigurdsson tapped into an empty net after Shittu made a hash of clearing the danger.
Although QPR piled forward looking for an equaliser, they lacked creativity and deserved nothing from a poor second half.