Violent clashes occurred in the city prior to the match, with the bad blood spilling into Parc Olympique Lyonnais as supporters fought in the stands.
Besiktas fans, situated in the top tier of the stand, also reportedly launched fireworks and other objects down into the Lyon section below.
Kick-off was delayed by over half an hour as the pitch was cleared.
After emerging from the tunnel, players from both teams clapped the fans before the match got underway.
Read the full article on eurosport.co.uk: Violence delays start of Lyon-Besiktas match as fans take refuge on pitch