Both sets of players had emerged to warm up when objects began to rain down from the stands, causing an unexpected delay to the start of proceedings in France.
Alongside an image of supporters entering the field of play, Lyon posted a tweet reading: "Projectiles and firecrackers thrown from the tops of the stands have forced fans to take refuge on the pitch."
The match was expected to kick off at 8.05pm, but Uefa spokesman Pedro Pinto tweeted that there would be a delay due to "crowd disturbances".
At 8.16pm, with no members of the public remaining on the playing surface, Lyon tweeted that a revised kick-off time would be announced "in several minutes".
Then at 8.36pm, Pinto tweeted: "Authorities at Stade de Lyon confirm Europa League match between OL and Besiktas can take place. Kick off expected soon."
The game eventually kicked off 45 minutes late.