Rooney ensured that United kept alive their slim hopes of catching Chelsea at the top of the Premiership with two clinical finishes in the first half at White Hart Lane.
Jermaine Jenas pulled Tottenham back into the game, but United showed their class to come away with all three points and keep Chelsea waiting a little bit longer for their second consecutive Premiership title.
Tottenham enjoyed a lively start to the game and could have opened the scoring after just two minutes.
Michael Carrick's fantastic 30-yard pass picked out Aaron Lennon down the right.
The winger crossed into the box and Jermain Defoe's slight touch saw the ball fly inches past the post.
And Carrick was again the provider on six minutes when his cross picked out Michael Dawson whose shot was superbly kept out by Edwin Van der Sar in the Manchester United goal.
The hosts were made to pay for those missed opportunities when Rooney broke the deadlock for United on eight minutes.
Ruud van Nistelrooy set away Ronaldo down the left. The Portuguese winger crossed in first time for the England striker who slid the ball into the corner of the net.
Defoe was unlucky not to snatch an equaliser on 15 minutes when he weaved his way into the box and drilled a low shot which produced a superb save from the Dutch keeper diving low to his left.
Ronaldo could have added a second for United on 34 minutes. Gary Neville played a superb ball into the box which caused all kinds of problems for the Spurs defence.
Ronaldo rose highest, but his close-range header flew just past the post.
Young-Pyo Lee had a moment to forget for the home side on 36 minutes when he gifted Rooney his second goal of the game.
The Korean defender was dispossessed in the box by fellow countryman Ji-Sung Park. Rooney picked up the loose ball and had the easy task of firing the ball past Paul Robinson.
United defender Nemanja Vidic was lucky to stay on the pitch on 50 minutes when Carrick burst free into the United half and was brought down on the edge of the box by the Serbian defender.
But referee Mark Halsey ignored the strong pleas of the home fans and only showed a yellow card.
Tottenham refused to lie down and forced their way back into the game on 53 minutes.
Robbie Keane's corner saw Vidic head the ball straight against Rio Ferdinand. The rebound fell kindly to Jenas who made no mistake in firing the ball into an empty net.
Van Nistelrooy should have put the game out of Tottenham's reach on 57 minutes when he broke the offside trap and took the ball around Robinson.
But home defender Michael Dawson produced a fantastic sliding challenge to deny the prolific forward.
And the Dutch striker came even closer on 86 minutes to adding a third. Neville's cross picked out van Nistelrooy whose close-range shot came back off the post.
But United held on and there could yet be another twist at the top of the table before the season comes to a climax.