Rooney's double blast took his goal tally for the season to 32, although this was far from a one-man show. Dimitar Berbatov was also on song, scoring United's third goal with all the action coming in the second half.
Rooney broke the deadlock 20 seconds after the restart. The England man found Nani on the left side of the Cottagers' penalty area.
Nani rolled the ball back into the centre of the box where Rooney scored with a well-placed right-foot shot into the bottom right corner of the net from 12 yards.
United had to wait another 38 minutes before doubling their lead.
Berbatov was the provider from a tremendous run when he cut in from the right in between Fulham defenders Nicky Shorey and Chris Baird, before crossing for Rooney to score with a right-foot near-post shot from ten yards.
Rooney began the move which led to the third goal a minute before the end of normal time.
His raking cross field pass found substitute Ji-Sung Park on the right and the South Korean's cross was headed in by Berbatov at the near post from six yards.
United could have had more goals, but found visiting goalkeeper Mark Schwarzer in fine form.
On the half hour, Berbatov set up Rooney on the edge of the Fulham box and he hit a tremendous shot which Schwarzer brilliantly turned away at full stretch.
The Australia international made an equally impressive stop in the 82nd minute.
A surging run by Darren Fletcher into the Fulham penalty area ended with him hitting a ferocious shot from 12 yards which Schwarzer superbly turned over at full stretch.
United's former Fulham goalkeeper Edwin van der Sar did not have a serious shot to save, although Bobby Zamora had two clear cut chances to score.
In the 38th minute, he collected a Danny Murphy pass and raced beyond United defender Rio Ferdinand, but then chipped his shot over van der Sar and the bar from 15 yards.
Zamora also fluffed another good chance in the 74th minute when he capitalised on a slip by Nemanja Vidic to go clear, but the Serb recovered brilliantly to rob the striker in the United box.