Lyon secured a 2-1 win over the Turkish side following a dramatic comeback, but it was the incidents pre-match that took centre stage.
Pictures and videos emerged on Twitter of fans clashing in the stands before pouring onto the pitch.
The Europa League quarter-final first leg was due to kick off at 8.05pm but was delayed about 45 minutes..
“Projectiles and Fireworks launched from the top of the stands require supporters to seek refuge on the lawn,” Lyon tweeted.
Police officers as Lyon fans invade the pitch and fans clash in the stands Lyon v Besiktas: Fans clash as violence erupts in stands at Europa League tie Thu, April 13, 2017
Lyon's Europa League quarter-final against Besiktas was delayed due to a pitch invasion and fighting in the stands prior to kick-off
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Lyon and Besiktas' Europa League tie was delayed due to fighting in the crowd
Lyon's Europa League match with Besiktas has been delayed after crowd trouble
Fans clash in the stands ahead of Lyon v Besiktas
The game between Lyon and Besiktas has been delayed due to crowd trouble
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— Pedro Pinto (@PedroPintoUEFA) April 13, 2017
— Olympique Lyonnais (@OL) April 13, 2017
BEŞİKTAŞ TARAFTARI LYON TRİBÜNÜNÜ BASTI ! pic.twitter.com/4AatviGJp8
— Beşiktaş_Ulan (@Besiktas_ulan03) April 13, 2017
Lyon Stadı'nda olaylar çıktı! Beşikaşlılar ile Lyonlular birbirine girdi! Sahaya yüzlerce taraftar indi… pic.twitter.com/HmheDM0IOO
— FOX HABER (@FOXhaber) April 13, 2017
— A Spor (@asporcomtr) April 13, 2017
— Beşiktaş JK (@Besiktas) April 13, 2017
The disturbances came just two days after bus explosions caused Borussia Dortmund's Champions League game with Monaco to be put back by 24 hours.
Security had been stepped up in Brussels where Manchester United faced Anderlecht tonight.
But problems in the stands in Lyon meant the Besiktas tie was delayed.
Besiktas fans are believed to have started the trouble in Lyon
Police in Lyon try and calm the crowd
Lyon and Besiktas fans were on the pitch after fighting broke out in the stands
BT Sport commentator Jonathan Pearce is at the stadium and said: "We still have no word of a kick-off time but Lyon president Jean Michel Aulas has gone into the crowd to try and calm the situation. He looks emotional.
“The electronic board in the stadium stadium says that the kick-off will be 'in a few minutes'."
The game did finally kick off 45 minutes late after the police were able to clear the pitch.
Besiktas tweeted: "In Lyon, the teams came on the field, players gentleman's images. The football match will begin shortly. Achievements"
There was trouble in the city of Lyon earlier today and it is believed Besiktas fans began the fighting in the stadium and were throwing fireworks towards the Lyon supporters.