Harry Redknapp urged Rangers to keep the faith in the build-up but even he will be hard pushed to remain positive after this latest defeat.
As fate would have it, a player the QPR boss had hoped to bring to Loftus Road during the January transfer window did the damage in west London.
Crouch, a man Redknapp has managed four times before, put Stoke ahead late in the first half and was pulled back by Clint Hill for the second-half penalty which Jon Walters fired home.
Rangers did look dangerous in spells but whenever they found the target another of Redknapp's former players was in the way, with Asmir Begovic in inspired form.
The result moves Stoke six points clear of danger and could well act as a catalyst in their bid to beat the drop, although QPR's fate looks bleaker than ever.
Perhaps with half an eye on next season, Redknapp made five alterations to the QPR starting line-up today.
Robert Green came in for regular number one Julio Cesar, while Tal Ben Haim was given his first league start by the Rs.
Adel Taarabt, the star of Rangers' 2010-11 promotion season, was another recalled and was quick to make an impact.
The Moroccan needed just 36 seconds to create the afternoon's first chance, coming close with a fizzing drive from distance.
Taarabt again threatened in the sixth minute with a 25-yard free-kick that curled just wide.
It was far from a dominant start by QPR, though, and Stoke were enjoying relative joy when they voyaged forward.
Cameron Jerome's pace was causing Rangers' back-line a particular headache as he linked up well with Crouch.
City also threatened on the break and QPR had Jose Bosingwa to thank for getting back to deny Ryan Shawcross.
Play was swinging from end-to-end, with a blocked Loic Remy header followed by a tame Jerome strike across the face of goal.
Charlie Adam became the first player booked for a late challenge on Remy, who was proving a nuisance for the visitors.
The France international has impressed since arriving from Marseille in January and forced Begovic into a low save after making himself room for a shot.
Remy sent a right-footed snapshot inches wide moments later as the home side pressed for an opener, which would have come at the other end was it not for Green's fine reactions.
The QPR goalkeeper did well to palm away a fantastic half-volley from Crouch and, keen not to be outshone, opposite number Begovic soon stopped a goalbound Bosingwa free-kick.
One goalkeeper was to concede before the break, though, as Marc Wilson burst forward after winning the ball at the halfway line.
The recalled defender sent a fine through ball to Jerome, who did well to hold play up before squeezing a cross past Christopher Samba into the path of Crouch to slot home.
Samba came close to making amends with a side-footed volley that went just wide before the half-time whistle was met by a chorus of boos.
Jamie Mackie replaced Andros Townsend when the teams re-emerged for a second half that began in scrappy fashion.
Begovic had to be alert to thwart a low Remy shot 10 minutes after the restart and then pulled off an incredible save to deny Samba, only to see the offside flag already raised.
Both sides soon lost players to injury as Taarabt and Wilson were forced off, before Samba saw a header denied.
However, any remaining QPR hope was extinguished in the 77th minute.
After Robert Huth hit the post with a header, referee Chris Foy pointed to the spot after adjudging Hill to have tugged back Crouch in the box.
Having been made to re-take his penalty, Walters coolly slotted home down to Green's right in front of the 1,181 visiting fans.
QPR fans streamed out after Stoke's second but did not miss much as the match ended without much action of note.
"We are staying up" chanted the City fans at the final whistle, while QPR's remaining support let the players know of their clear displeasure.