The match was marred by an on-field scuffle that spilled into the stands. A video shows an Everton fan walking towards a brawl between players and punching the Ligue 1 outfit's goalkeeper Anthony Lopes on his head.
Lyon were leading the game 1-0 and the incident took place midway through the second half when Everton captain Ashley Williams pushed Lopes against the hoarding behind the goal post. Lyon players surrounded the former Swansea City man, before Everton players rushed to the scene.
This is when an Everton fan carrying a toddler left his seat and walked towards Lopes and punched him on his head. Williams was shown only a yellow card and missed being sent off in the Merseyside club's latest defeat in the European competition.
Williams admitted that his emotions were high, while Everton were pushing for three points against Lyon.
"It's what happens, it's football. It is what it is. 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," Williams told BT Sport.
According to the Guardian, Everton are likely to face a Uefa disciplinary action for the ugly brawl, which also saw a fan getting involved in the incident.
Nabil Fekir gave the French club an early lead after converting from the penalty before Williams' 69th minute header helped Everton equalise. However, it was Bertrand Traore's back heel six minutes later that proved to be the difference between the two sides in the end.