Athletic Club produced a stirring second-half fightback to dent Atalanta's hopes of automatically reaching the last 16 of the Champions League, while boosting their own play-off ambitions.
Gianluca Scamacca's first-half header had given the hosts a deserved half-time lead, before Ernesto Valverde's side took control in the second period.
Gorka Guruzeta levelled just before the hour mark, with substitute Nico Serrano adding their second and Robert Navarro placing a third past home goalkeeper Marco Carnesecchi.
While Atalanta pulled a goal back late on, when Ademola Lookman provided fellow substitute Nikola Krstovic with a tap-in, it proved too little too late.
The result leaves the Bilbao club 23rd in the table on eight points with a home fixture still to come against Sporting on Wednesday, 28 January (20:00 GMT).
Atalanta head into their final league-phase match, having dropped out of the top eight into 13th.
As one of eight teams on 13 points, the Italians will likely need a victory at Belgian champions Union Saint-Gilloise to progress directly into the knockout stage.
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