The teenage striker struck his 13th goal of the season midway through the second half to reduce Chelsea's advantage to nine points.
And Rooney also had a hand in United's second which sealed victory as his cross from the right was sliced into his own net by City defender Richard Dunne.
Having lost 3-1 and 4-1 in their last two away matches at City, United, now unbeaten in 16 league games, certainly had a few scores to settle.
But without the injured Ruud van Nistelrooy, Louis Saha and Alan Smith, and with Ryan Giggs and Cristiano Ronaldo only fit enough for places on the bench, the fear was that United would not have the firepower to keep on Chelsea's shirt-tails.
And in the goalless opening period that looked to be the case as United created only two clear-cut chances with Rooney going close each time.
City ought to have finished the first half in the lead as Kiki Musampa forced a great early save from Roy Carroll and Steve McManaman fired wide when it looked as though he could not miss.
The deadlock was finally broken in the 68th minute following a good passing move which ended with Gary Neville firing in a low near post cross. Rooney managed to get in front of Dunne to find the net with a low shot.
The breakthrough was quickly followed by a second United goal as Rooney's cross from the right was put past his own keeper by the hapless Dunne.
City refused to concede defeat and in a strong finish should have scored. Carroll denied Musampa for a second time with a great save while Robbie Fowler blazed over from inside the six-yard box. Antoine Sibierski and substitute Jonathan Macken also wasted decent openings.
Deep into stoppage time Giggs almost added a third for United when his shot beat City keeper David James only to strike an upright.