The incident took place in the 38th minute with both Turkish and French spectators throwing firecrackers and smoke-bombs onto the playing surface despite them being separated.
Police were sent into the stands to restore order in the stadium as the game was put to a stop for some minutes.
Both Galatasaray boss Fatih Terim, and club captain Fernando Muslera as well as Dimitri Payet were seen appraoching the fans in an attempt to calm the situation.
There were still sound of firecrackers going off in the stands when the match resumed with about eight minutes remaining in the first half.
Approcahing the final whistle, Galatasaray forward Mbaye Diagne and Marseille defender William Saliba also went into a misunderstanding on the pitch as both grabbed each other and jostled near the sideline but were separated by team-mates before they received bookings.
Marseille have been involved in an incident of this nature for a number of times this season, as fans stormed the pitch in a Ligue 1 game when Payet was hit by a bottle and threw it back into the crowd before fans angirly invaded the field, leading their Ligue 1 match at Nice to be abandoned.
Another fans unrest were also witnessed when Marseille defeated Montpellier in August during their first Ligue 1 fixture this season with fans throwing bottles onto the pitch.
