The match on 25 January at the Vélodrome was delayed for 35 minutes after a firecracker was hurled from the stands.
"It hit me on the back, then it fell and exploded next to my foot," said Marseille's Jordan Amavi who was standing on the touchline near his teammate Kevin Strootman and the assistant referee.
"Because of the serious nature of the events, the commission is going to look into the matter throughly. During that time the Vélodrome will be closed," said a statement from the French league's disciplinary commission.
The 67,000 seat Vélodrome - one of the most celebrated venues in European football - is renowned for the fervour of the fans.
A ban on supporters is the latest blow to Marseille.
They have won only one of their last 11 games and have been eliminated from the Coupe de France and the Coupe de la Ligue.
Marseille, whose next home game is against Bordeaux on 5 February - lie eighth in Ligue 1 after 20 games following the 2-1 loss to Lille.