Captain Sergio Ramos had handed a 1-0 lead to Man United conceding an own goal in the 48th minute.
Nemanja Vidic was denied a goal by the post in the 21st minute during the first half of the game.
In the 67th minute, Luka Modric drove a powerful shot from 20-yards to bring Real Madrid on level terms. Modric had came in as a substitute for Alvaro Arbeloa only seven minutes earlier.
Cristiano Ronaldo winner helped Real Madrid beat Man United 2-1 in the second leg of Champions League as they advanced to quarter-finals on 3-2 goal aggregate.
Ronaldo scored the winner in the 69th minute slotting home a low cross from Gonzalo Higuain. He did not celebrate and instead held his hands up almost apologetically.
Referee Cuneyt Cakir dished out a sensational red card on Nani who caught Alvaro Arbeloa with a high boot while vying for the ball in the 56th minute.