Lyon have been charged with "insufficient organisation" of their supporters after crowd disturbances seriously delayed the start of Thursday's 2-1 Europa League victory over Besiktas, who were also charged.
Tension between rival supporters in the east-central French city spilled into the Parc OL before the scheduled kick-off, with a barrage of projectiles from the upper tiers forcing fans on to the pitch and casting the viability of the fixture into doubt.
The trouble eventually abated and the teams were able to start the game 45 minutes later than planned, with Lyon recovering to beat the Turkish champions 2-1 in the quarter-final's first leg.
President Jean-Michel Aulas and human resources manager Vincent Ponsot have blamed the visiting fans for the trouble but UEFA has not picked sides, citing both clubs for the presence of fireworks.
A statement from the governing body on Friday evening said disciplinary proceedings had been opened, with Lyon charged on the basis that fireworks were ignited, stairways were blocked, and that there was insufficient organisation regarding the segregation of supporters.
A further charge applied to fans invading the pitch after Lyon's late winner, which was scored by Jeremy Morel, but not to the earlier incursions onto the field.
Besiktas were charged over the "setting off of fireworks", the "throwing of objects" and "crowd disturbances."
The date of the hearing of the UEFA control, ethics and disciplinary body is still to be determined.
Earlier, Lyon defender Christophe Jallet admitted he had been saddened by the disturbances.
While previewing Sunday's Ligue 1 trip to Bastia via Lyon's official Twitter account, France right-back Jallet said: "We watched what happened with a lot of sadness.
"We spent the entire 45 minutes worrying and wondering if there would be a new kick-off time.
"We play football to experience strong emotions but not like those we felt yesterday. It was a real shame to witness such a commotion.
"It's not every day that you get the opportunity to play in a European quarterfinal so it's very unfortunate that all this has happened around the game."