The Portuguese forward saw a penalty saved by Willy Caballero after 22 minutes, but made amends shortly afterwards as he blasted past the Argentine goalkeeper following a short pass from Xabi Alonso.
Ronaldo reached the landmark in just 197 games for the Spanish side and has now scored 54 goals in 53 games this season at club level.
THE TOP 10 GOALSCORERS FOR REAL MADRID
With 200 goals, Ronaldo is sixth in the list of the club's all-time top scorers, eight behind legendary Mexico striker Hugo Sanchez.
Madrid, meanwhile, needs to beat Malaga to stop Barcelona from claiming La Liga on Wednesday night.