Rooney's deflected first-half effort saw off a dogged Royals outfit, who worked hard but lacked the class to fashion an equaliser.
Reading now look certainties for relegation, sliding seven points adrift of safety with one game fewer than United to save themselves, their decision to axe Brian McDermott akin to shuffling deck chairs on the Titanic.
Thirteen points will do it for Sir Alex Ferguson's men to clinch a record 20th championship - and given one of their remaining games is against nearest challengers Manchester City, who lost at Everton, they might not even need that.
Rio Ferdinand had a hand in the opening goal as he nipped in to intercept Garath McCleary's poor pass, advanced into the open space and went round a static Mikele Leigertwood before feeding Rooney just to his left. The striker took aim and once his shot flicked off Alex Pearce, goalkeeper Stuart Taylor had no chance of keeping it out.
Either side of Rooney's goal, Danny Welbeck went close on a couple of occasions and Robin van Persie tried his luck from 20 yards. These are not the most productive of times for the Dutchman though, who has now scored once in his last 10 games.
The visitors threatened before the break, when Hal Robson-Kanu let fly with a shot David de Gea would not have reached if it had been on target.
They should have had a chance to equalise immediately after it though when Nemanja Vidic shoved Adrian Mariappa over inside the box. Reading appealed for what TV replays showed to be a clear foul but referee Lee Mason was unmoved.
United failed to profit from their good fortune, with Welbeck and Ashley Young going close either side of a wild effort from Van Persie that flew out from a throw-in. Taylor then repelled a well-struck free-kick to keep the former Arsenal man out.
Whilst Rooney did fire over from long-range, the hosts gave Reading enough hope to believe an equaliser was possible. It did not come though. And as certain as it appears United will end the season champions, Reading looked destined the finish it in the npower Championship.