The forward completed Madrid's comeback in the 69th minute at Old Trafford to secure a 3-2 aggregate win for the Spanish champions.
Madrid had gifted United an opener at the start of the second half when Sergio Ramos scored an own goal.
But the game swung back in the visitors' favour in the 55th minute when Nani was sent off for a studs-up challenge on Alvaro Arbeloa.
Madrid seized control of the match with two goals in two minutes, with Ronaldo setting up Luka Modric for a powerful equaliser in the 67th before getting on the score sheet himself.
In Germany, Borussia Dortmund beat Shakhtar Donetsk 3-0 to reach the quarter-finals for the first time since it won the competition in 1997.
Felipe Santana scored in the 31st minute, Mario Goetze in the 37th and Jakub Blaszczykovski in the 59th to complete the victory that sent the German champions through 5-2 on aggregate.
The Champions League is Dortmund's only chance to win a trophy this season.
Dortmund achieved the domestic double last season but have been eliminated from the German Cup by Bayern Munich and are 17 points behind the Bavarians in the Bundesliga.
Dortmund were without central defender Mats Hummels, down with the flu.
But his replacement Santana got Dortmund rolling with the first goal of the match.