Frankfurt charged with 'racist behaviour' after fan unrest in Champions League fixture
The charges come after Marseille's police prefecture said it had informed UEFA that some visiting fans "performed Nazi salutes in the away section" during the game.
Frankfurt were also charged for the "throwing of objects" by their supporters, who were accused of setting off fireworks as well as other "acts of damage" around the game at Marseille's Velodrome stadium.
The home side were charged with a series of similar offences including crowd disturbances as the French club lost the Group D encounter 1-0.
"Disciplinary proceedings have been instigated in accordance with Article 55 of the UEFA Disciplinary Regulations," a UEFA statement said.
"The UEFA disciplinary bodies will decide on the matter in due course."
One German supporter was injured and 17 people were arrested on the sidelines of the game, according to authorities in the Bouches-du-Rhone department of southern France which includes Marseille.
Around one thousand police officers had been mobilised for the game which came just five days after a Europa Conference League match between Nice and German side Cologne was marred by trouble which left four people hospitalised.
During Tuesday's match, one German supporter was hurt by a flare thrown from the stands and taken to hospital, police said.