Athletic Club mounted an impressive recovery after the interval to undermine Atalanta’s pursuit of a direct place in the Champions League last 16 and to strengthen their own chances of reaching the playoffs.
The home side had been in control before the break, with Gianluca Scamacca rising to head them in front and reward their first-half dominance.
Momentum swung decisively after the restart, as Ernesto Valverde’s players imposed themselves and gradually turned the contest in their favour.
Second-half turnaround proves decisive
Parity arrived shortly before the hour, when Gorka Guruzeta found the net to bring the visitors level and shift belief within the Bilbao ranks.
Fresh legs then made the difference, with substitute Nico Serrano completing the comeback before Robert Navarro extended the advantage by beating Marco Carnesecchi for a third time.
Although Atalanta responded late on, as Ademola Lookman set up fellow replacement Nikola Krstovic for a close-range finish, the late effort failed to change the outcome.
Table implications and final fixtures
The victory moves Athletic Club into 23rd position with eight points, leaving them still in contention ahead of a remaining home match against Sporting on Wednesday, 28 January, kicking off at 20:00 GMT.
For Atalanta, the setback drops them from the top eight down to 13th place going into the final round of league-phase fixtures.
Level on 13 points with seven other sides, the Italian team are likely to require success away to Belgian champions Union Saint-Gilloise if they are to secure automatic qualification for the knockout stage.