Ronaldo argues with the linesman after he was not awarded a penalty in Madrid (Photo: Rueters)
The Portuguese star was substituted with around 20 minutes left in the match in Calderon after aggravating a leg muscle injury.
Ronaldo will undergo tests to determine the seriousness of the injury, Real Madrid said on their website.
He suffered the original injury during the club's 7-0 drubbing of Malaga on 3 March.
It is not clear whether he will be able to join the Portuguese squad for the friendly internationals against Chile and Finland later this month.