Atleti recalled a handful of more experienced names following their loss to Elche in midweek, but they were under pressure within three minutes as Gorka Guruzeta stretched to reach a ball over the top, but Jan Oblak had the tight angle covered to stop the shot.
That was the only effort from either side in the first quarter of the match, which saw Alex Baena denied a penalty after going down in the box.
But, midway through the first half, the visitors made the second shot count, when Inigo Ruiz de Galarreta’s corner was met by a bullet header from Dani Vivian.
Having become only the fourth side to concede first at home to Athletic this season, Los Colchoneros finally created something with nine minutes of the half to play, as Giuliano Simeone’s cross from the right was met by a firm Alexander Sorloth header, which the striker planted straight at Unai Simon.
Other than that, the hosts continued to look disjointed and were whistled off at half-time by a frustrated home crowd.
But those jeers turned to cheers just four minutes into the second half, when a low centre from Baena from the left took a couple of deflections but still found its way to Antoine Griezmann, who poked home the equaliser.
Five minutes later, and the match had been turned on its head, as Simeone ran hard through the middle of the park before finding Sorloth, who played an expert one-two with Baena before finishing coolly.
The Norwegian almost had a brace moments later, but this time he fired wide when aiming for the top corner.
The hour mark saw momentum swing back in Lehoiak’s favour - Guruzeta did superbly to bring the ball down at the edge of the box before firing a whisker wide, then an Oihan Sancet effort needed a firm block, before Dani Vivian rose highest at a set-piece again, but this time his header went over.
In the final 10 minutes, the Bilbao side looked to be running out of ideas, as long-range strikes from Vivian and Mikel Vesga didn’t come close to troubling Oblak.
In stoppage time, Nahuel Molina picked out Sorloth on halfway, and the striker raced away unchallenged to seal the points for Atleti, who avoided suffering five consecutive league losses for the first time since 1942.
The Basque club grabbed a consolation in the dying seconds through a Guruzeta header, but they missed the chance for a first double in 26 years and remain three points shy of the top six.
Flashscore Man of the Match: Alexander Sorloth (Atletico Madrid)
