Disturbances marred Marseille's 2-1 win at San Mames on Thursday.
Before the match, a stadium security guard suffered a neck wound caused by a sharp object, though his injuries were not serious.
Once inside the stadium, Marseille supporters lit flares, some of which were dropped from their second-tier location onto the Athletic fans beneath, with charges ultimately brought against the club for setting off and throwing fireworks, as well as for general crowd disturbances.
Lyon are also being charged for the same offences, as well as for blocked stairways and racist behaviour. Lyon's case will be dealt with on May 31, while Marseille will find out their fate on Thursday.
The news comes just a day after the two sides faced each other in a dramatic Ligue 1 game which was blighted by unsavoury scenes involving the two sets of players.
Memphis Depay's late winner settled a fractious match 3-2 in Lyon's favour, but things reached boiling point near the end when Marcelo and Marseille's Adil Rami became involved in an off-the-ball altercation.
That incident then appeared to be the main cause of the two sets of players becoming embroiled in a tunnel brawl after full-time, with Marseille goalkeeper Steve Mandanda accusing Lyon of showing a lack of respect.
"What's a pity is that we talked a lot this week," he told Canal+. "I read, I heard, and in the end we blew up. That is the unfortunate thing.
"At the end of the game, I think we're all at fault for a little fighting. There is still a little anger because they [Lyon] do not respect the opponent that much."
That result moved Lyon to within two points of third-placed Marseille in the hunt for the final Champions League spot.