The Europa League quarterfinal between Lyon and Besiktas was delayed for 45 minutes when supporters were forced to invade the pitch after projectiles and firecrackers were thrown from the upper deck and into the stand below.
Besiktas looked sharp despite the lengthy delay to kick-off and wasted no time in testing Lyon's resolve early on - Marcelo seeing an overhead kick saved by Anthony Lopes before he was denied again by Mouctar Diakhaby.
Jean-Michel Aulas, the Lyon president, was among officials on the pitch attempting to restore order.
They also threw metal objects and fireworks at the French fans in the lower stands.
Turkish pro-government media were blaming French fans for Thursday night's trouble.
Police have reported the arrest of a dozen fans from both teams, with five officers and two supporters suffering minor injuries after fighting broke out inside the Parc Olympique Lyonnais before kickoff.
The report also described clashes between supporters and the authorities outside the stadium: "The incidents appear to involve Besiktas Ultras, with a large section of the travelling support wearing black t-shirts".
Around 15,000-20,000 Turkish fans had been expected in Lyon for the game taking place at a stadium situated in an area of the city which is home to many people of Armenian origin.
Ryan Bable strike put Beşiktaş ahead in the first half, however, Lyon came from behind to take the lead after the French side notched an equalizer when Corentin Tolisso poked home from close range. A minute later, Besiktas goalkeeper Fabri gifted Lyon a victor when he took a backpass close to goal and tried to trick his way past the onrushing Jeremy Morel.
Lyon have been hit by four UEFA charges, Besiktas three.
"It's not every day that you get the opportunity to play in a European quarter-final so it's very unfortunate that all this has happened around the game".