The striker was called into action at the other end soon after when he did well to clear Pepe's header from a corner.
However, the Frenchman made no mistake on 35 minutes as he nodded in at the back post from Ronaldo's cross.
Malaga started strongly after the break, but Benzema nearly doubled the home side's lead when his snatched finish flew over the crossbar.
Ronaldo was foiled by Wilfredo Caballero in the Malaga goal on the hour as the goalkeeper tipped away the winger's low drive.
Benzema was a constant threat for Madrid, but he somehow missed the target from only a couple of yards with 20 minutes to play.
Despite Madrid's dominance throughout the match, Malaga grabbed an equaliser in injury time when Cazorla fired an unstoppable free kick past Casillas and into the top corner.
Jose Mourinho's side now lead rivals Barcelona by eight points in the table.