Both teams' bans have been deferred for a probationary period of two years, European soccer's governing body UEFA said in a statement on its website.
Ugly scenes in the crowd delayed kick off at the Parc Olympique Lyonnais by 45 minutes.
Lyon were charged with insufficient organisation and a breach of safety regulations as their fans blocked stairways, set off fireworks and invaded the pitch after the home team's second goal completed a comeback 2-1 win.
Visiting Besiktas were charged with their fans setting off fireworks, throwing objects and crowd disturbances.
Clashes between rival fans started hours before the kick off after around 15,000 Besiktas supporters arrived in Lyon, marching through the city centre and lighting flares.
Read the full article on eurosport.co.uk: Besiktas and Lyon handed suspended European bans by UEFA