When tensions finally subsided the match went ahead with Lyon winning 2-1.
Soccer fans of rival teams rioted before a Europa League quarterfinals match at the Parc Olyimique Lyonnais stadium in Lyon, France, on April 13 (video below).
Ligue 1 side are facing charges for launching fireworks, blocking stairways, insufficient organisation and a pitch invasion after the late victor.
Besiktas' three charges relate to the setting off of fireworks, the throwing of objects and crowd disturbances.
Pinto then tweeted: "Authorities at Stade de Lyon confirm @Europa League match between @OL and @Besiktas can take place".
"The supporters are waving big Turkish flags".
"Projectiles and fireworks launched from the stands require fans to take refuge on the pitch", Lyon tweeted.
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The game has now kicked off after the police managed to clear the pitch.
Lyon president Jean-Michel Aulas was also seen urging supporters to calm down and return to their seats but following full-time the 68-year-old claimed there had been no choice but to "flee".
Trailing at halftime, Lyon scored twice in the last 10 minutes to win 2-1.
The incident came just 24 hours after some Leicester City supporters were filmed singing distasteful war songs and clashing with police before their Champions League quarter-final tie with Atletico Madrid.
It will be all to play for in the second leg in Genk after the Belgians lost an entertaining clash against Celta Vigo 3-2 in Spain.
Tuesday saw Borussia Dortmund's team bus hit with explosives in Germany.
A number of stewards appeared to be wounded in the violence and were led away by police and medics, while one fan had blood streaming down his face.
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