Shaun Goater all but ended Millwall's hopes of a play -off place as the FA Cup finalists' winless run extended to seven games.
The Lions are four points adrift of sixth place with just two games remaining and the home side were unlucky enough to hit the woodwork twice, yet still failed to break down a resolute Reading.
Goater struck in the 16th minute when he volleyed in John Salako's corner past Andy Marshall.
It was after Millwall player-manager Dennis Wise had gone close with a cheeky chip over visiting keeper Jamie Ashdown, which flew just high of the bar.
But Reading looked the more hungry of the sides and were unfortunate not to be ahead ten minutes into the game when Adrian Williams' close-range effort was palmed over the bar by Marshall after Danny Dichio had cleared Dave Kitson's shot off the line.
Paul Ifill came agonisingly close to levelling the scores two minutes from half-time when his 25-yard free-kick was tipped on to the post by Ashdown.
It was the last piece of caution for the next 20 minutes as Reading seemed content to soak up the Millwall pressure.
It took the 67th minute introduction of teenager Peter Sweeney for Millwall to look like scoring and he almost had an immediate impact when his shot flew over the bar with almost his first touch.
He then put Ifill through only for the winger to mistime his kick.
A minute from time he teed up a free-kick from just outside the area only for it to loop against the post with the keeper beaten.
Millwall assistant manager Ray Wilkins said: "If I'm to be honest that's us gone. We'll keep battling away but if we have to be realistic, we are out of it."
Reading boss Steve Coppell sympathised with his former Manchester United team-mate Wilkins and added: "It's difficult to have the dual agenda and to concentrate on all those games, no matter what anyone says."