QPR hung on for a vital point which keeps them in second place in the Division Two table.
Tempers flared late on with Rangers boss Ian Holloway sent from the dug out by East Yorkshire referee Paul Robinson after the drama of a sending off and a twice taken penalty.
Tranmere's Gary Jones got clear in the 76th minute but was brought down by Clarke Carlisle. Marcus Bignot and Arthur Gnohere were involved and were both cautioned and for Bignot it meant a red card as he had also been booked in the 33rd minute.
Eugene Dadi netted from the spot into the left-hand corner but the official then ordered the penalty to be retaken because of encroachment by Gareth Roberts.
This time Dadi saw his shot strike the right-hand post. The ball rebounded to Jones who brought a stunning save from Rangers keeper Lee Camp.
Tranmere on the night were the better side. It was their fifth match without conceding a goal.
They could have been three goals ahead inside seven minutes with Tyrone Loran volleying wide, Jones being blocked out by Camp and Dadi heading into the side-netting.
Dadi got clear in the 38th minute only to be denied by Camp. Then when he sprung the Rangers defence in the 55th minute his shot grazed the outside of a post.
Kevin Gallen got in Rangers' best first half effort which was punched out by John Achterberg in the 12th minute.
And the striker was unlucky in the 72nd minute when an effort was headed off the line by Ian Sharps.
Later Paul Furlong blazed wide with a free-kick but generally the visitors were well-contained by a competent home side.
Holloway later demanded a hearing from the referee. Rangers midfielder Gareth Ainsworth said: "I can understand the manager's frustration. It was a harsh penalty decision and it was justice when it did not count." Tranmere boss Brian Little said: "My only complaint would be why the penalty was retaken. I would like to see the video.
"We had a lot of chances on the night and it was a good all-round performance. It should have been three points but we have got one and I am not totally disappointed."