The game, which will be replayed behind closed doors, was called off after Marseille's Dimitri Payet was hit by a bottle thrown from the stands of Lyon's Groupama Stadium.
Lyon, whose president Jean-Michel Aulas criticised the referee's decision to end the Nov. 21 game, remain 12th in the standings, now with 22 points from 16 matches.
"Any act of violence against a player, especially a major player, exposes the club responsible to a loss of points," Sebastien Deneux, the president of the LFP disciplinary committee, said.
"The committee also took into consideration the actions of the Lyon club immediately after the incidents. I would like to remind you that the Disciplinary Committee cannot take sanctions against fans directly, but is there to judge the responsibility of the clubs."
Ligue 1 has been marred by fan violence this season.
Nice were docked two points, one of them suspended, after serious incidents during their game in August against Marseille, when visiting players clashed with home fans who pelted them with missiles and stormed on to the pitch.
The northern derby between RC Lens and Lille was hit by crowd problems in September, with the start of the second half delayed after rival fans threw objects at each other before people ran on to the pitch, prompting riot police and stewards to intervene.