Peter Crouch's strike late in the first half gave the Potters an unfamiliar half-time lead, after the home side had wasted several opportunities.
The R's came out of the blocks much faster in the second period, but lacked a cutting edge, as they have throughout much of their ill-fated campaign.
And they were made to pay as Jonathan Walters' penalty sealed a vital victory for the Potters, who are now up to 15th, and all but condemned QPR to Championship football next season.
The visitors, who previously had netted only once in the first half of their previous 13 games in the Premier League, started the match in the ascendancy, with Cameron Jerome looking a threat down the channels.
Eventually, the R's did get themselves into the game, with Loic Remy having a few efforts on target, both easily saved by Asmir Begovic.
Harry Redknapp's men, who also won several free-kicks in promising positions, were made to pay for their wastefulness by a swift counter-attacking opener from the Potters.
Marc Wilson won a tackle and sent a clever ball down the channel which Jerome latched onto, took his time, and drilled a low cross which Crouch side-footed in to give Stoke the half-time advantage.
The hosts finally created a clear-cut opportunity just after the interval, and it was that man Remy, who jinked past two Stoke defenders but saw his powerful effort well smothered by Begovic.
That miss, and several other wayward efforts from good positions cost the R's, when referee Chris Foy pointed to the spot after Crouch was pulled down by Clint Hill reacting to Robert Huth's header, which came back off the post.
Walters stepped up, and, despite being forced to retake, fired low past Rob Green into the bottom corner.
The goal killed off any resistance that the home side were offering, and they must now start to plan for life in the second tier of English football next season, whilst the Potters' second win of the year gives them a little breathing space in the basement battle.