QPR fully deserved their victory after pressing the Bluebirds throughout the 90 minutes.
Cardiff welcomed back Steven Thompson from injury, while Paul Parry passed a late fitness test. Chris Gunter came in at full-back for his league debut.
Former City favourite Gareth Ainsworth was in the Rangers starting line-up but he only lasted 14 minutes before being replaced by Nick Ward after suffering an ankle injury.
Both sides seemed to have difficulty controlling the ball on a greasy surface but Lee Cook worked an opening and Neil Alexander in the Cardiff goal had to palm away for a corner.
A period of Rangers pressure was lifted midway through the half when a long ball from Darren Purse was chased by Michael Chopra but keeper Simon Royce raced smartly out of goal to hack clear.
An error by Alexander from a Stephen McPhail back pass almost gifted Dexter Blackstock the opening goal on the half hour.
The keeper's attempted clearance was blocked by the Rangers striker but Alexander recovered to push the goalbound shot behind for a corner.
It was the 39th minute before City mounted a sustained attack when Gunter appeared on the left wing and his cross brought panic to the QPR defence. When the ball was cleared it gave Parry a chance for a run but his 20-yard shot zipped over the crossbar.
Neither side made changes for the second period but it was Rangers who would have been happier following their gritty first-half performance.
In the 55th minute City's Kevin McNaughton cut in from the left before firing a dipping shot that struck the crossbar with Royce well beaten.
That seemed to galvanise the table-toppers into action and leading scorer Chopra fired over when well placed.
Parry had the ball in the net in the 53rd minute but the flag was up for offside.
The Bluebirds finally paid the penalty for a below par performance in the 88th minute when Ward worked his way down the right before crossing into the danger area and substitute Jones stretched out a leg to divert the ball into the net.