About 100 fans of the French club clashed with riot police at Karaiskakis Stadium before the match against Olympiakos on Tuesday. The Greek team won 3-1.
UEFA said Thursday that its disciplinary panel will judge the case on Nov. 22.
UEFA also charged Olympiakos for "insufficient organization" at the match, plus for fans throwing missiles and aiming laser-pen beams at players.
Olympiakos faces a further mandatory fine after five players were shown yellow cards.