It was the Portuguese forward's first goal of the season and a third consecutive league victory for Real that lifted them to the top of the table ahead of Wednesday's matches.
Both teams had a player sent off with around half an hour remaining and Espanyol were reduced to nine late on.
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Real coach Jose Mourinho criticised the poor state of the pitch after the game and also complained about the packed calendar, Tuesday's match coming after his players were in action in the Champions League on Wednesday and in La Liga on Saturday.
"All things considered I am coming away satisfied because it's not easy playing on a potato field, it's not easy playing every two days and it's not easy playing an opponent who has nothing to lose," the Portuguese said at a news conference.
"Putting all those factors together and despite the fact that my team did not play a good match I am satisfied," he added. "We have to improve but above all we need to rest."
The visitors began brightly on a pleasantly warm night at the Bernabeu and an unmarked Jose Callejon volleyed just wide of Iker Casillas's goal in the sixth minute.
Real responded immediately when Mesut Ozil sent Angel Di Maria clear and the Argentina winger's curled strike was palmed narrowly over the crossbar by goalkeeper Carlos Kameni.
Espanyol's solid start was spoiled just before the half hour when Luis Garcia handled a Ronaldo free kick in the wall and the referee pointed to the spot.
