The Red Devils may yet have to negotiate a second leg at Old Trafford on March 10 but two second-half goals from Rooney means last season’s beaten finalists are firm favourites to book a place in the Champions League quarter-finals.
Not even the concession of a third-minute opener for AC Milan, created by Beckham for Ronaldinho, could derail Alex Ferguson’s troops, although they were forced to endure some nervy moments at the end after Clarence Seedorf hauled Milan back into the tie five minutes from time.
It took a fortunate Paul Scholes effort to bring United level before the break.
But, after surviving another spell of Milan pressure after half-time, Rooney stamped his class on the contest, scoring his first two European goals of the season to take his overall tally to 25.
Ronaldinho put the hosts ahead in the opening moments but Paul Scholes grabbed a fortuitous equaliser and two goals from Rooney put United in charge.
Clarence Seedorf’s late goal pegged Alex Ferguson’s side back but Rooney felt they were worthy winners.
The England striker said: “It was a disappointing start but after that we did well to get back into it. The second half we stepped it up and we fully deserved to win, we were always the better side.
“When we went 3-1 up I thought it was only us that looked like scoring. The goal keeps Milan in the tie but 3-2 in the San Siro is a great result.”
Rooney cut a frustrated figure through much of the first half as Milan largely dominated and he hinted it was displeasure with the referee’s performance that was riling him.
“Some people were not doing their job right,” he said. “But I got the booking and I learned from it.”
The match was David Beckham’s first against his former employers, and Rooney had some generous words for his England team-mate.
“You can see the quality he’s got,” the striker said. “The experience, set-pieces, he’s a great player.”
Ferguson admitted United’s last trip to the San Siro, when they were thrashed 3-0 in the semi-finals in 2007, may have played on their minds following Ronaldinho’s early goal.
He said: “There was a catalogue of errors. The start to the game helped them and we started to get nervous – the last time we came here we conceded two early goals. But once we were settled, I thought we did okay.”
Beckham warned there is more to come from Milan. “We had three really good chances but you have to put those chances away,” he continued. “The second half the game opened up and they put them away. But it’s not over. We’ll go to Manchester and it’s going to be a tough game.”
United were transformed in the second half, and Ferguson knew Rooney would be the key.
“The most important thing was better use of the ball and to use Rooney more. I felt he had the beating of them and he was fantastic tonight,” the United boss said.
“We were coasting at 3-1 then it was a carnival end to the game. It’s made it a game when it shouldn’t have been a game. We’ve got to do a job at Old Trafford now. Let’s go out and win it.”
What was ultimately a more than satisfactory night for United began disastrously. Ronaldinho fired Milan into an early lead after Patrice Evra’s acrobatic attempt to clear a Beckham cross fell to the Brazilian, whose shot deflected off Michael Carrick and past the wrong-footed Edwin van der Sar.
Milan continued to force the issue and Ronaldinho, Luca Antonini and Klaas Jan Huntelaar twice came agonisingly close to finding a second.
United’s equaliser was more than a little fortunate. After a Darren Fletcher cross, Scholes missed the ball with his right foot, the ball striking him half way up the shin of his standing left before rolling past the stranded Dida.
Milan’s response was admirable, given what a blow that away goal was, United’s first in five away games against a fellow European heavyweight.
Andrea Pirlo forced a one-handed save out of Van der Sar with a 30-yard free-kick, then the 39-year-old Dutchman required every inch of his massive frame to flick a goalbound Ronaldinho effort round the post.
Yet a minute after what turned out to be an inspired substitution, Rooney break his European duck. Antonio Valencia, who had just replaced Nani, was the provider, sending over a cross from the right that allowed Rooney to steer a header back over Dida into the opposite corner.
Now the age in Milan’s legs began to tell. And when Darren Fletcher chipped another cross into the box, Rooney stole between defenders to head home once more.
It seemed victory and progress was assured, so Ferguson will be livid at the Seedorf effort five minutes from time that ensured an uncomfortable ending and gives Milan a flicker of hope for the return, when Michael Carrick will be unavailable following his dismissal deep into stoppage time.