Ronaldo scored his 36th goal of a remarkable season in the first leg quarter-final against AS Roma to put United in the driving seat going into the second leg at Old Trafford next week.
The Portugal winger got on the end of a chip from Paul Scholes to head past Roma's Brazilian goalkeeper Doni in the 39th minute.
Sir Alex Ferguson's side made it 2-0 in the 67th minute when Park Ji-Sung headed the ball into the area at the back post.
It resulted in a mix-up between Doni and Christian Panucci with Rooney on hand to knock the ball home and stun the crowd at the Stadio Olimpico.
In the other quarter-final of the night, Barcelona secured a 1-0 away win against Schalke thanks to teenager Bojan Krkic's 12th minute tap-in after good work from former Arsenal player Thierry Henry.
AS Roma 0-2 Manchester United
Schalke 0-1 Barcelona
