A second consecutive La Liga defeat for Real leaves them already six points adrift of leaders Barcelona after just three games as they were 2-0 winners over Athletic Bilbao earlier in the day thanks to a double from Neymar here.
Atletico got off to the best possible start as Tiago headed home Koke's corner, but Real were soon level as Cristiano Ronaldo won and then converted a penalty midway through the first-half.
However, with suspended coach Diego Simeone watching on from the stands, Atletico grabbed all three points 13 minutes from time when Arda Turan swept home Juanfran's low cross.
Atletico went in front with the first clear opening for either side as Koke's in-swinging corner was met with a bullet header from Tiago at the near post.
The conceding of the goal led to large swathes of the Bernabeu booing Real captain Iker Casillas when he touched the ball.
However, the hosts responded well to going behind and after Miguel Angel Moya had produced a stunning save to claw away a Gareth Bale free-kick, Ronaldo levelled from the penalty spot after he had been felled by Guilherme Siqueira.
And Moya denied the Frenchman once more with a great low save after Benzema had powered a Ronaldo cross towards goal just before the break.
Real's momentum towards the end of the first-half petered out after the restart, though, as Atletico began to take control after the introduction of substitutes Turan and Antoine Griezmann.
Turan was inches away from restoring Atletico's lead when he cut inside Alvaro Arbeloa and curled the ball just wide 15 minutes from time.
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