Jose Antonio Camacho's side took a shock lead at the Bernabeu on 20 minutes when Iranian midfielder Javad Nekounam outleapt Fabio Cannavaro to nod Jaroslav Plasil's cross past Iker Casillas.
An error by goalkeeper Roberto Fernandez gifted Real an equaliser just after the break, a long-range Sergio Ramos shot spooning into the net off his hands, and Gonzalo Higuain netted shortly after, tapping home Arjen Robben's low cross.
"I come back here after four years to try to play well for my team and I get sent off because of mistakes by the referee," Juanfran said in a radio interview. "It hurts a lot."
Real's win follows Barcelona's 5-0 thrashing of Deportivo Coruna at the Nou Camp on Saturday.
"Barcelona are playing very well and producing some magnificent football," Real coach Juande Ramos said at a news conference.
"Madrid is not playing as well but has been achieving good results for the last month and that creates confidence and allows you to play much better."
Fernando Llorente's penalty in added time snatched a 3-2 win for Athletic Bilbao against fourth-placed Valencia as the Basque side twice came from behind in an ill-tempered clash at the San Mames. Malaga thumped Espanyol 4-0 to climb to seventh ahead of Deportivo in eighth and Athletic in ninth.
