With less than a minute on the clock, Ruud van Nistelrooy inadvertently flicked on Mariano Pernia's corner and striker Sergio 'Kun' Aguero stooped to nod home the simplest of chances.
The home crowd was stunned into near-silence as the Argentine youngster scored the first goal of the new season.
But Los Merengues levelled the scores on 15 minutes when Sergio Ramos' pinpoint cross was headed home by Raul much to the veteran striker's delight.
Later in the first half, Ramos almost scored himself but his header from Wesley Sneijder's corner came back off the bottom of the post and Atletico managed to clear the ball to safety.
Madrid were without new arrivals Arjen Robben and Gabriel Heinze but it was another of their summer signings who gave them victory with 10 minutes to go.
Guti teed up Wesley Sneijder from a free-kick and the former Ajax midfielder, now sporting David Beckham's old squad number 23, found the net with a low shot which took a slight deflection past Atletico keeper Leo Franco.
So, a winning start in the league for Real's new coach Bernd Schuster who has a tough act to follow after previous coach Fabio Capello was sacked despite winning last season's title.