كتب : Amro Hassan
A second half Simao free kick cancelled out Ruud Van Nistelrooy's ninth minute strike, but Gonzalo Higuain converted a late penalty kick to hand Real the win.
The game saw two red cards at both ends. Luis Perea was given his marching orders on 30 minutes for a second caution while Van Nistelrooy saw a straight red nine minutes later.
In the ninth minute, Van Nistelrooy silenced the Atletico faithful after successfully capitalizing on Leo Franco's deadly error.
Real, who were without Guti and Mohamadou Diarra due to injury held on to their lead until the 89th minute when Simao equalized through a brilliant free kick.
But on 93 minutes, Real won a penalty after a reckless tackle from John Heitinga Royston Drenthe and Higuain made no mistakes from the spot.
The win lifts Real to top of the Liga table with 14 points while Atletico stay seventh with nine points.