Ronaldo was on the end of several heavy challenges as Madrid earned the three points courtesy of Angel Di Maria's 53rd-minute strike.
Pepe said: "It's very important to take three points. Cristiano received a very late challenge. It's also important that we handled the game well being one man down."
Sergio Ramos said: "The referee's decision after the challenge on Cristiano was unfortunate, but it's also true these things happen in games. Winning was what mattered tonight, but we must keep learning."