Victory left QPR two points above the relegation zone ahead of the final round of matches, when manager Mark Hughes takes his team to champions-elect Manchester City -- one of his former clubs -- next Sunday.
Joyful Rangers fans invaded the pitch after the final whistle but their side are not yet mathematically safe from the drop.
Former France striker Cisse settled the match when he stole in at the back post to convert Anton Ferdinand's flick-on.
It wrapped up a great afternoon for Rangers, owned by Malaysian businessman Tony Fernandes, after Bolton Wanderers, who had threatened to drop them into the bottom three, were held to a 2-2 draw by West Bromwich Albion.
Stoke had the better of the play early on, with chances for Cameron Jerome and Peter Crouch, although QPR playmaker Adel Taarabt tested Potters goalkeeper Thomas Sorensen with a 25-yard free-kick.
The visitors twice nearly went ahead after the break, Crouch making a mess of a free header and Ricardo Fuller curling a shot just wide.
Hughes then made two more substitutions, bringing on Jay Bothroyd and Shaun Wright-Phillips late on and his changes led to QPR's goal.
Wright-Phillips' shot deflected wide, creating a QPR corner. Taarabt's cross was nodded on by Ferdinand and Cisse scored from close range to send the crowd wild.
Crouch missed a chance to grab an equaliser in the four minutes of added time as QPR held on for a valuable win that was followed by a mass pitch invasion before the Rangers players returned to salute their supporters.
Source: AFP
Source: AFP