After a quiet start to the fixture, QPR thought they had broken the deadlock in the 18th minute when Clint Hill converted a corner from Joey Barton, despite the effort of Wanderers goalkeeper Adam Bogdan.
However, referee Martin Atkinson and his assistant failed to spot that the ball had crossed the line.
The away side had chances to draw themselves level before the break, but Shaun Wright-Phillips shot over, while Nedum Onuoha saw his effort blocked by Bogdan.
Just three minutes after the restart, QPR did haul themselves level. Wright-Phillips threaded a pass for Cisse, who was allowed to convert past Bogdan despite appearing to be in an offside position.
Substitute Jamie Mackie went close to grabbing a second for QPR 12 minutes from time, but his goal-bound effort was blocked on the line by Wanderers defender David Wheater.
With just four minutes remaining, Ryo Miyaichi slipped a pass through to Klasnic, who took one touch before slotting the ball beyond an advancing Paddy Kenny in the away goal.
QPR piled on the pressure in stoppage time, but they were unable to find a second equaliser.
Wanderers move out of the relegation zone with the three points.