Athletic Bilbao inflicted Qarabag's first defeat in the current edition of the Champions League.
In the third round match of the Champions League phase, Bilbao won 3:1.
Qarabag of Azerbaijan, who had two wins in the first two matches, took the lead with a goal from Leandro Andrade in the first minute of the match.
But Gorka Guruzeta, who scored twice on Wednesday night, equalized in the 40th minute.
Robert Navarro scored in the 70th minute for 2:1, while Guruzeta settled the challenge with the 88th minute goal.