Payet was hit as he was about to take a corner kick after five minutes and both teams were sent to the locker room as the game was suspended for nearly two hours.
It was announced that the match would resume but referee Ruddy Buquet then declared that the safety of the players could not be guaranteed and the match was abandoned.
After being hit by the bottle, Payet fell to the ground and left the field with an ice pack on his head.
Ligue 1 has been marked by crowd problems this season.
A match between Marseille and Nice in August was abandoned under similar circumstances when Payet was hit by a bottle and sent it back into the crowd, prompting the Nice fans to assault.
A game between RC Lens and Lille in September was delayed after rival supporters threw objects at each other and then rushed onto the pitch before riot police and stewards had to intervene.