The ugly scenes were sparked by an Ashley Williams foul on goalkeeper Anthony Lopes, who was then pushed in the melee towards the advertising hoardings at the Gladys Street end, where an irate fan carrying a young child slapped him on the head twice.
Instigator Williams lost his head during the scrap as was seen swinging his arms in an aggressive manner towards Lyon midfielder Lucas Tousart. Williams was very fortunate to escape with just a yellow card and will almost certainly face retrospective disciplinary action when UEFA review the footage. But he played down the incident when quizzed by BT Sport after the final whistle.
'It's what happens, it's football. It is what it is. It's just what happens, it's football and stuff happens. It was one of them things I suppose," Williams said.
Lyon forward Bertrand Traore was also booked after confronting the fan who struck his team-mate. The incident occurred midway through the second half when the score was 1-0 to the visitors. Williams later equalised for Everton, only for Traore to restore the Lyon lead which had earlier been established by Nabil Fekir.
Everton have now taken just one point from their first three group games in the Europa League this season. The defeat - Everton's sixth in their last 10 games in all competitions - piled more pressure on manager Ronald Koeman, who criticised the standard of officiating.
"There was a certain irritation in that moment by Ashley because he's that player who likes to win and who cannot deal with a lot of disappointments. But I think the mistake was also by the referee because they make a lot of theatre and he did nothing," he said.
"(Nabil) Fekir was I think 10 times on the floor diving [and] not even a yellow card. And that grows our irritation and even extra time... It's five minutes. We had six substitutes and that's three minutes. We had the fight and that was maybe two minutes and they had I think eight times injuries in the game and it's five minutes... come on, please," he added.
Speaking on BT Sport, pundit Jermaine Jenas suggested that Williams' meltdown was perhaps the result of the defender struggling to deal with what has been a hard period in his career.
"The last couple of weeks will probably go down as the toughest weeks of his career. Getting knocked out (of the World Cup) by Wales in the way that they did, a lot of that fell on his shoulders in terms of the way they went out," Jenas said.
"(He is) captain tonight and the pressure that Everton are going through, it seemed to me like that all came together and he lost control in one specific moment," he added.