"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.
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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.
WALES FRUSTRATION AFFECTING WILLIAMS
Everton manager Ronald Koeman said on Friday that Williams had acted out of frustration born partly from Wales's failure to qualify for the World Cup and needed to control his emotions better.
"I understand his situation yesterday," the manager told a press conference ahead of Sunday's Premier League home game against Arsenal.
"His personal situation, it was difficult after (being knocked) out of the World (Cup following the qualifiers) with Wales. He had some mistakes that cost a goal but I like that mentality.
"From frustration you get maybe more aggression and that's not bad. But you need to control yourself."
The defender, who scored an equaliser for Everton minutes after the incident, and Lyon striker Bertrand Traore, who got the winner for his side, received yellow cards for their parts in the struggle.
Koeman also praised his skipper for his leadership on the pitch.
"He showed his face yesterday, he played well," he added. "He was a captain on the pitch and of course in the situation of the brawl he needs to control himself.
"But okay, on one side I understand frustration, disappointment, because everybody was disappointed."
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.
(Writing by Aditi Prakash and Simon Jennings in Bengaluru; editing by Amlan Chakraborty and Pritha Sarkar)
