Ernesto Valverde's side, fifth, had Gorka Guruzeta and Nico Williams struck second-half goals to deservedly secure the points for the intense Basques who dominated at a jubilant San Mames.
Athletic drove Diego Simeone's visitors back in the first half, testing Atletico goalkeeper Jan Oblak on multiple occasions. The Slovenian made a superb save low at his near post to deny Guruzeta early on, and another to block Nico Williams' effort after he broke through on the left.
Oblak was saved by the frame of his goal on two occasions, with both brothers Inaki and Nico Williams striking the woodwork. Athletic's best chance of the first half came from the penalty spot but Oihan Sancet smashed high and wide.
Athletic got the breakthrough they deserved quickly at the start of the second half, with Ander Herrera crossing to the back post, where Guruzeta was unmarked to finish with ease.