Atletico were thwarted by an Espanyol side who have made a strong start to the season under Mexican coach Javier Aguirre, and who have moved up to fifth on the back of the result.
A cagey first-half saw neither side able to muster a shot on target, so it was of little surprise that the goal came through unconventional means.
The goal came in the 54th minute when the ball deflected into the net off the outstretched leg of Atletico goalkeeper Thibaut Courtois.
The Belgian attempted to keep out a deep cross from Juan Fuentes but the ball bounced off his arm and into the net.
Despite a late onslaught, it was not to be as Atletico dropped their first points of the season.