Ronaldo had struck twice in quick succession in the first half to put Madrid on their way to a 10th consecutive home win this season, but he was then handed his marching orders in the 70th minute.
The world's most expensive player, who was also sent off against Almeria in December after picking up two late bookings, was shown a straight red card after catching Patrick Mtiliga in the face with a flailing elbow as he attempted to escape from the Malaga defender.
"I cannot complain about the commitment of the players. The collective performance is what interests me. That's what makes the goals. We have to improve individually and collectively," said Real coach Manuel Pellegrini.
"I'm not happy, we were playing as individuals but we kept the defensive intensity and we scored two good goals. We had a really good first half."
On the dismissal of Ronaldo, the Chilean said that he did not see the incident but acknowledged that the impending suspension of the Portuguese star would be a loss.
"I could not see it from the bench. It would be a serious loss and the referee will have to determine how serious his act was."