Bastia fans ran on to the pitch and attempted to attack Lyon players in the warm-up before their Ligue 1 match.
Lyon keeper Mathieu Gorgelin was caught in the middle of a group of pitch invaders, before stewards held off fans while players were rushed down the tunnel and a gate closed behind them.
The game in Corsica kicked off almost 55 minutes late as a result.
It has been a difficult week for Lyon with crowd trouble before their game with Besiktas on Thursday.
Fans clashed before their Europa League match in France, with kick-off delayed by 45 minutes as a result. Lyon went on to win 2-1.
Lyon face four Uefa charges from that game, for the setting-off of fireworks, blocking stairways, insufficient organisation and a pitch invasion after a late winning goal.