Tony Pulis' men are now two points behind leaders Bristol City after Mikele Leigertwood (2) and Akos Buzsaky condemned them to their second away defeat without scoring in five days.
To make matters worse, Andy Griffin was astonishingly sent-off by referee Andy D'Urso for a non-existent foul on Hogan Ephraim, whose QPR side consolidated their mid-table position and showed the form that big-spending owners Flavio Briatore and Bernie Ecclestone hope will see them scrape into the play-off places.
The course of the game was shaped by a dramatic 45 seconds involving Rangers midfielder Leigertwood.
On 12 minutes the summer signing from Sheffield United deflected Liam Lawrence's dangerous free-kick onto his own bar, the ball hitting Lee Camp on the back and bouncing on the line before being hacked away.
Emboldened by his lucky escape, Leigertwood then strolled upfield and, when the ball broke to him 30 yards from goal, showed commendable technique to arrow a stunning left-footed half-volley inside Steve Simonsen's right-hand post to record his third goal for the club.
His fourth was not long in coming as Rangers made Stoke look anything but a side vying to go top of the table.
It was another composed finish from Leigertwood as he smashed the ball into the roof of the net after Rowan Vine had expertly cushioned Buzsaky's cross into his path.
D'Urso then took centre stage, sending off Stoke captain Griffin for what he thought was a two-footed tackle on Ephraim.
Griffin was furious, and with good reason, as replays showed that the former Newcastle man's foot simply bounced high after landing on the ball, and the decision provoked understandable anger from Pulis and his players.
The game was all over 11 minutes into the second half when the hosts scored their third goal after a superb passing movement ended with Patrick Agyemang - who was offside in the build-up - unselfishly setting up Buzsaky for a low drive across Simonsen and into the far corner of the net.
Both sides threatened after that, but QPR saw the game out safely to leave them just eight points off the play-off spots.