Ashley Williams was fortunate not to see red when he needlessly shoved Lyon goalkeeper Anthony Lopes to the floor under a high ball in the 64th minute of the Toffees' 2-1 defeat, before squaring up to Bertrand Traore.
As the fracas spilled off the pitch towards the advertising hoardings, a man holding a child reached over and appeared to slap Lopes, while other fans were seen grabbing at the visiting players.
One individual has been banned by Everton, who have also raised the issue with Merseyside Police.
But European football's governing body have taken a dim view, charging the Premier League club with "aggressions by supporters against players - Art. 16 (2) (H) of the Disciplinary Regulations".
A statement added: "This case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on 16 November."
Everton were fined €10,000 in September after crowd trouble in their match with Hajduk Split.
Just three minutes after the fracas, Williams cancelled out Nabil Fekir's fifth-minute penalty with a thumping header, but Traore's flick won the points for Lyon and piled more pressure on Everton boss Ronald Koeman.
Ashley Williams is shown a yellow card after pushing Anthony Lopes and causing a mass brawl 😳 pic.twitter.com/4BRWvCQ10p— BT Sport Football (@btsportfootball) October 19, 2017
After the match, Lopes reported he was hit by a fan but sought to play down the incident.
"It was no big deal, it happened and that was it. For me, it seemed to wake up the fans and they seemed to love it," he told reporters.
"I don't think it is part of the English atmosphere to hit an away player, but it was like this. But I am proud that we were strong at 1-1 and we won the game despite everything. It was a very proud night for us."
Williams was led away from the fracas by Everton goalkeeping coach Patrick Lodewijks before he and Traore were booked.
"It's what happens, it's football. It is what it is," the Wales international told reporters.
"It's high emotions. We want to win the game, they want to win the game and stuff happens. That was just one of those times."