The French Professional League (LFP) told the club to close their north and south enclosures while a full inquiry was launched by the body's disciplinary commission.
The sections of the ground will remain closed until October 15, the date when the Marseille board will also meet.
"The seriousness of the facts...and the context of recurrence" sparked the decision, said disciplinary commission president Sebastien Deneux.
Last Sunday's game was halted after an hour and the players instructed to return to the dressing rooms as objects, including bottles and cups, rained down from the stands
The return of Lyon's Mathieu Valbuena to face his former club had already made for a charged atmosphere with the France international, roundly booed throughout, already the target of missiles when taking corners.
The violence prompted fears to be raised around the security measures for next summer's Euro 2016 championships which will be held in France.