The German had a rush of blood in first-half stoppage time when he raced up field to try to shutdown a counter-attack, only to be left red-faced as Yannick Carrasco took the ball around him and knocked it into the empty net.
Barcelona could not find their way back into the match, leaving coach Ronald Koeman once again facing more questions over the direction of his side.
Atletico then nearly went in front as Barcelona keeper Ter Stegen produced a fine reaction stop to save Saul Niguez's first-time strike.
The hosts were denied by the frame of the goal on 12 minutes after Marcos Llorente was played in and his shot came back off the crossbar.
Following such an electric start, the tempo of the match dropped as half-time approached, only for the game to come to life again in stoppage time.
Ter Stegen came racing out of his goal to try to shutdown an Atletico counter-attack from a long pass upfield, and Carrasco took the ball around the stranded Barcelona keeper before knocking it into an empty net from 25 yards.
Atletico made a tactical change with 15 minutes left when Llorente was substitute for Diego Costa, the striker fit again following his own injury lay-off.
Barca coach Koeman sent on Portuguese winger for the closing stages, replacing Griezmann, but there was to be no late drama.
Atletico, who are now 24 games unbeaten, move level on 20 points with leaders Real Sociedad, while Barcelona are down in 10th place.