Jesper Lindstrom's first-half goal guided Eintracht to their first Champions League victory, extending their unbeaten away run in Europe to seven matches.
However, what should have been a momentous night for Oliver Glasner's team was marred by off-pitch events, with social media footage seemingly showing the two sets of fans aiming fireworks at one another in the stands.
Further footage appeared to show a supporter making a Nazi salute within the stadium, leading the club to respond in the aftermath of their victory.
An Eintracht statement read: "The club dissociates itself completely and utterly from the one isolated incident that occurred during the run-up to the UEFA Champions League match between Olympique de Marseille and Eintracht Frankfurt, where a gesture resembling a Nazi salute was made.
"Anti-Semitic ideas are totally opposed to the club's categoric and immutable values and roots.
"The person who can be seen on the video and who has yet to be identified reported of their own accord to the Eintracht Frankfurt fan representatives during the first half of the match and emphatically denies the accusation of anti-Semitic motives.
"Eintracht Frankfurt will be conducting a detailed investigation of the events and the behaviour of the person involved."
Asked about the unsavoury scenes after the match, Eintracht coach Glasner said: "I focus on the sporting aspect, my role is sport. But I believe that these idiots do not belong to football, nor to the world.
"We all agree that they should not be given too much importance. I prefer to talk about football. This aggressiveness is not just a football problem, it is a general problem today."