United, despite going ahead through an early goal from Cristiano Ronaldo, had looked doomed to defeat when two goals from Milan's brilliant Brazilian Kaka cruelly exposed the Red Devils' weakened defence.
But, cometh the hour, cometh the man, and seconds before the 60th minute Rooney levelled the scores.
Then, with the game almost a minute into injury time, the England man struck again with the most dramatic of winners.
It had taken United eleven minutes to open the scoring in their ritual 7-1 slaughter of AS Roma a fortnight ago, but it was only five minutes before they broke the deadlock against the northern Italians.
Ryan Giggs curled the most tantalising of corners into the Milan box.
Ronaldo, standing six yards out on the far post, got in a header which Milan goalkeeper Dida could only punch up in the air.
Dida's fumbling effort to rescue the situation only made matters worse and the ball ended up in the net along with United defender Gabriel Heinze.
But United could not reinforce their early advantage and were punished by Kaka.
The loss of Gary Neville, Rio Ferdinand and Nemanja Vidic was always going to be hard to bear against such quality opposition and so it proved in the 22nd minute.
Kaka raced onto Clarence Seedorf's pass from the left to shrug off the attention of John O'Shea before brushing away Heinze's attempt at a tackle and scoring with a crisp low shot beyond United goalkeeper Edwin Van der Sar and into the net from ten yards.
But United's defending turned into pure farce a quarter of an hour later.
Dida's long goal kick found Kaka out on the left. The Brazilian moved up a gear when he raced inside to beat Heinze, whose attempt to retrieve the situation was ended when team-mate Patrice Evra barged into him and knocked him over.
Kaka was left to run clear and coolly placed his shot past Van der Sar and into the net from twelve yards.
United should have equalised three minutes after the interval when Giggs produced another superb corner which left Michael Carrick free at the far post, but the England man missed a sitter when he drove his shot wide from only six yards out.
United kept on going and finally levelled the scores in the 59th minute.
Carrick released Paul Scholes and his glorious chip into the box found Rooney, whose shot from twelve yards went in off the legs of Dida.
United stormed forward in a bid to gain the edge for the second leg in Milan next week.
Giggs sent three free-kicks narrowly wide, while Darren Fletcher forced a fine save from Dida, but it looked as if United would have to settle for a draw.
Then as the game ticked well into the first of two minutes of injury time, Rooney struck again.
Giggs found Rooney free on the right and the England man collected the ball in his stride before hitting a ferocious right-foot shot from the right side of the Milan penalty area and beyond Dida and into the bottom corner of the net at his near post.
Advantage United, but with Evra suspended for the second leg after collecting a 42nd minute booking, the case for the defence will again fall on the quality of the attack.