Merseyside Police are also investigating the brawl on the pitch between players from both teams, while Everton have banned one individual.
"Disciplinary proceedings have been opened following the UEFA Europa League group stage match between Everton FC and Olympique Lyonnais (1-2), played on 19 October in England," UEFA said in a statement on Friday.
The governing body added that the English club had been charged with "Aggressions by supporters against players" under Article 16 (2) (H) of its disciplinary regulations.
Everton captain Ashley Williams sparked off the trouble in the 64th minute when he shoved Anthony Lopes into the advertising hoardings after the Lyon goalkeeper had collected the ball from a corner.
An all-out melee ensued with players from both sides getting involved, while at least one fan behind the goal was caught on video throwing punches at a Lyon player before stewards intervened.
Everton issued a statement saying they had banned an individual from future matches after reviewing footage of the incident and would be making a formal complaint to Merseyside Police.
The force said its detectives would review footage and speak to witnesses to establish what, if any, offences had been committed.
Everton manager Ronald Koeman blamed poor refereeing for the scuffle near the Gwladys Street End stand in comments made after the match.
"I think the irritation grows in the game for our players and in my opinion that was the problem by the referee," said Koeman, whose team lost 2-1.
"The referee was Dutch but he didn't do anything against the theatre of some of the Lyon players. (Lyon captain Nabil) Fekir in the first half dived 10 times.
"I understand with my players, that comes out of frustration. I don't know what happened but I can understand it."
Defender Williams, who scored an equaliser for Everton minutes after the incident, and Lyon striker Bertrand Traore, who scored the winner for his side, received yellow cards.
The loss increases scrutiny of Koeman, whose team sit bottom of their group with no wins in three Europa League games and on a two-game winless streak in the Premier League, where they are 16th in the standings.
Everton host top four contenders Arsenal in the league on Sunday.
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