Les Gones secured qualification from Group I with last night's victory, while also ensuring that the La Liga outfit remain rooted to the bottom of the group.
Last year's beaten finalists are now without a win in any of their four fixtures.
"It's not easy to come to Bilbao and win," said Gourcuff. "We showed great spirit, the team never gave up, even during the difficult moments.
"It was important to show that spirit against Athletic. We played some good football and to score three goals is impressive too."
Lyon travel to Sparta Prague for their next fixture.