A game devoid of clear chances appeared to be heading towards a goalless draw as QPR threw everything at Stoke in a desperate finale.
But Stoke's resistance was finally broken when Adel Taarabt's corner was glanced on by Anton Ferdinand to Cisse, who tapped in at the far post to raise the roof in West London.
With QPR closing their campaign at the Etihad Stadium the Hoops enter the final weekend in 16th place, two points clear of Bolton, though they can also be caught by Wigan and Blackburn, who have games in hand.
QPR could – and should – have found themselves behind inside five minutes when Peter Crouch climbed high to nod the ball into Cameron Jerome’s path, but the striker snatched at his shot, slicing it wide from eight yards.
It was a glaring miss and QPR’s relief was illustrated in their willingness to get forward and open the scoring themselves – and Taarabt was the man most likely to put them ahead.
The Moroccan’s 13th minute free-kick bent around the wall and was heading for the bottom corner, but Thomas Sorensen pulled off a good save low to his right. Joey Barton seized upon the rebound but hammered it into the side-netting.
QPR enjoyed the best of the first half and Barton had two good chances in quick succession: the first a dipping effort from 20 yards that dropped just over, the second a header that was straight at the keeper.
Mark Hughes introduced Cisse early in the second half but it remained a tight affair as Stoke stubbornly kept Rangers out, with Cisse's impact negligible at first.
Stoke only had one shot on target in the whole game but could have opened the scoring when Taarabt lost the ball and Ricardo Fuller seized on the loose ball, curling it a whisker wide with his left foot.
But QPR created more in front of goal, and could have opened the scoring when Cisse met Taye Taiwo's cross from the left - but it was straight at Sorensen.
With the clock counting down, QPR went for broke and were rewarded right at the death - with Cisse scoring from close range to continue his remarkable run of scoring or being sent off in each of his seven appearances for QPR.
QPR have now won five home games in succession and have their fate in their own hands. But with Manchester City looking to secure the title, it could be a nervy 90 minutes for Hughes's side next weekend.