Arsenal F.C. qualified for the 17th successive season when Chile forward Alexis Sanchez scored in first-half stoppage time to give them a 1-0 win over Besiktas after a goalless draw in the first leg in Istanbul.
Swedish champions Malmo qualified for the first time with a 3-0 win over Salzburg, who held a 2-1 lead from the first leg.
Bundesliga side Bayer Leverkusen thrashed FC Copenhagen 4-0 for a 7-2 aggregate win while the tie between Ludogorets Razgrad and Steaua Bucharest went to extra time.
The group stage draw will be made in Monaco on Thursday.
Napoli, held 1-1 at home one week ago, went ahead through Marek Hamsik at the start of the second half before suffering a defensive collapse.
Aritz Aduriz levelled in the 61st minute and then put Athletic in front eight minutes later before and Ibai Gomez ended Napoli's hopes with the third in the 74th minute.