The scenes followed clashes between Besiktas supporters and French police outside the stadium ahead of kick-off.
Lyon and Besiktas happen to be charged by UEFA after their Europa League quarterfinal first leg was marred by crowd trouble.
The 1905 GMT start of the quarter-final first leg was delayed by 45 minutes as officials attempted to clear the Parc OL playing area of fans.
The French club have been hit with four charges, including "insufficient organisation" concerning the segregation of supporters, while Besiktas were charged with throwing projectiles and crowd disturbances.
The travelling fans came under attack from Lyon supporters armed with weapons in the terraces before the game had even started.
"With the intense fireworks, severe injuries and homemade bombs exploding around them our fans had only one option, to take refuge on the pitch", he suggested.
Jean-Michel Aulas, the Lyons president, called for calm inside the stadium via a loudspeaker.
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Turkish pro-government media were blaming French fans for the trouble.
The Thursday evening fixture in France saw the game delayed by 45 minutes as people spilled on to the pitch after fighting broke out between the rival fans and missiles were thrown.
"The supporters are waving big Turkish flags".
The return match is next Thursday in Istanbul which has a reputation as among the most hostile cities in Europe for visiting fans.
Dortmund's game against Monaco in the Champions League quarter-finals was postponed and played on Thursday.
After a pretty tumultuous week in the world of football, this is the last thing we wanted to see.
After a 9:50 p.m. (1950 GMT) kickoff in Lyon, Besiktas led at halftime through Ryan Babel's low shot in the 15th minute.