كتب : Amro Hassan
The result stretched the gap between Real and leaders Barcelona to six points, after the latter beat Athletic Bilbao 2-0 at Nou Camp.
While Real remain second in the table on 57 points, city rivals Atletico are fifth with 40 points.
Real coach Juande Ramos had to deploy midfielder Lassana Diarra at right-back due to Pepe's absence. Sergio Ramos played at centre-back alongside Fabio Cannavaro.
The home side's first chance came when Arjen Robben made a typical cut from the right and rifled a low shot which was saved by Leo Franco.
On 25 minutes, Sergio Aguero gifted Diego Forlan a great pass but the Uruguayan shot wide.
The former Manchester United man made up for his miss by putting Atletico ahead after receiving another Aguero assist and slotting a cool finish past Iker Casillas.
After the interval, Real pushed for an equalizer which exposed their defence, and Atletico could have added a second through one of their many counters.
However, the hosts finally got the goal they were looking for after substitute Gonzalo Higuain fed Klaas-Jan Huntelaar with a clever pass, and the Dutch striker made no mistake from close range.
Veteran hit man Raul could have notched a winner for Real, but the forward's bicycle kick went inches past Franco's post.
Watch the game's goals