After reported trouble outside Parc Olympique Lyonnais prompted police involvement, violence broke out behind one goal as players warmed up.
“Projectiles and fireworks launched from the stands require fans to take refuge on the pitch,” Lyon tweeted.
The game finally kicked off at 20:50 BST, 45 minutes behind schedule.
Lyon president Jean Michel Aulas went into the crowd in an effort to calm supporters.
When the French and Turkish sides eventually emerged, both sets of players clapped supporters all round the stadium, before going through brief warm-up drills before kick-off.
Authorities had labelled the fixture “high risk”, with around 500 police reportedly stationed at the stadium – more than double the usual amount.
Before Beskitas’ fixture against Greek side Olympiakos in the previous round, both clubs worked with Uefa and took the decision to ban away fans in a bid to avoid crowd trouble.
It is the third incident at a Uefa competition this week, following Tuesday’s bomb attack on Borussia Dortmund’s team bus and Wednesday’s clashes between Leicester City supporters and police in Madrid.