The Portuguese striker notched up his 25th goal of the campaign with a clinical finish from the edge of the area to see off the challenge from Malaga who battled hard but lacked a cutting edge.
Isco missed an excellent chance against his former club to give Real a more convincing win but they still picked up three valuable points in the title race with the only downside an injury to Karim Benzema.
He picked up a knock on his thigh after colliding with Ronaldo and had to be substituted but it is not thought to be serious.
Real now have 70 points, six more than city rivals Atletico Madrid who will look to reduce the gap when they take on Espanyol in the late game.
Barcelona, who are third on 63 points, face Osasuna on Sunday.
Earlier on Saturday, Rayo Vallecano beat Almeria 3-1 and Levante went down 1-0 at home against Celta Vigo.
(Reporting by Tim Hanlon, editing by Pritha Sarkar)