Sunday's (AEDT) hard-fought LaLiga contest was settled by a remarkable Yannick Carrasco strike in the third minute of first-half stoppage-time.
Ter Stegen, who was making just his third Blaugrana appearance in all competitions since returning from a knee injury, rashly set off in pursuit of the ball near the halfway line and was beaten to it by Carrasco, who kept his cool to find the empty net from distance.
It was a setback Barca could not recover from as it succumbed to a third league defeat of the season to remain 10th on the table, also losing Gerard Pique to a knee injury as Ronald Koeman's teething problems show no sign of easing.
🚑 More problems for @FCBarcelona – an horrific injury for @3gerardpique 😱 The depleted defence has another hole put through it!! @Atleti 1-0 @FCBarcelona— beIN SPORTS (@beINSPORTS_AUS) November 21, 2020
Watch LIVE on CONNECT @kayosports, @Foxtel & Fetch!! ▶️ https://t.co/w2AlZCRXkT#LaLiga | #AtletiBarcelona | #ATMFCB pic.twitter.com/fm5ZKaDRsK
The visitors had held their own in a lively start that saw Antoine Griezmann stab his volley just over before Ter Stegen dived away to his right to make a smart save from Saul Niguez's 20-yard drive.
Marcos Llorente came closest to an early breakthrough but blasted against the crossbar.
😱 OFF THE BAR!! @marcosllorente so close to the opener!! @mterstegen1 beaten, but not the frame of the goal!!@Atleti 0-0 @FCBarcelona— beIN SPORTS (@beINSPORTS_AUS) November 21, 2020
Watch LIVE on CONNECT @kayosports, @Foxtel & Fetch!! ▶️ https://t.co/w2AlZCRXkT#LaLiga | #AtletiBarcelona pic.twitter.com/1jZTISr7Uj
Jordi Alba interrupted a subsequent lull in proceedings with a sublime pass between Kieran Trippier's legs to send Lionel Messi through, yet he shot too close to Jan Oblak from a tight angle.
A nutmeg at the other end proved far more costly on the stroke of half-time, however, as Carrasco nudged the ball beyond Ter Stegen, who had inexplicably charged 40 yards from his goal to leave the Atletico winger with a straightforward finish into an empty net.
Clement Lenglet should have nodded Barca level 11 minutes after the restart but instead directed his header straight at a grateful Oblak and then saw centre-back partner Pique land awkwardly under a challenge, requiring assistance to depart down the tunnel.
Diego Simeone's men subsequently came on strong again, pushing Barca back the other way to see out a precious victory, and handing the Argentinian his first victory as a manager over his countryman Lionel Messi's club.
For a little over 10 minutes, this was an open, exciting affair with chances at either end. But Atletico, masters of the scrappy win, slowed the pace of the game expertly and seized on Ter Stegen's rare error in clinical fashion.
UEFA Champions League action resumes in midweek with Atletico at home to Lokomotiv Moscow on Thursday (AEDT), a day after Barca visits Dynamo Kiev.