During the break, flares were thrown back and forth between home and visiting fans in one stand. Home-made fireworks also exploded.
As security staff and police streamed towards the stand, spectators fled onto the pitch, preventing the resumption of the match.
The referee and players returned to the dressing room.
Ten minutes later, the public had returned to the stand after the intervention of the police and stewards and the call for calm from the stadium announcer.
But at 10:25 pm local time, the match had still not resumed.
The two teams were tied at 1-1. Gaetan Laura had given the hosts an early lead before Moussa Dembele levelled a minute before halftime.
The French season has been pockmarked by incidents involving fans.
Lyon have already been ordered to play two games behind closed doors and deducted a league point after their home game on 21 November was abandoned when Marseille's Dimitri Payet was hit on the head by a bottle thrown from the crowd.
That match is still to be replayed.