A hardcore section of home fans at Bastia's Armand Cesari stadium targeted Lyon's players as they warmed up before the game, causing it to be delayed by more than 50 minutes, and then again as the two sides went in for the break with the score at 0-0.
"We must stop, we must stop, they hit the players," Lyon coach Bruno Genesio told club president Jean-Michel Aulas in the corridors of the stadium.
Bottom-of-the-table Bastia are likely to have points deducted for the latest trouble involving their supporters.
Bastia were punished in February over racist abuse directed at Nice striker Mario Balotelli while the Nice team bus had its windows smashed.
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"Following the new incident at the end of the first period, the LFP decided to definitively stop the game between Bastia and Lyon," the French professional football league (LFP) said in a statement.
In the first incident Lyon players fled to the dressing rooms and the 1500 GMT kick-off was consequently delayed as captains and officials from the two teams and league officials held talks over whether the game should go ahead.
The trouble -- the second time in four days that Lyon have been caught up in football violence -- saw former Manchester United winger Memphis Depay reportedly among the Lyon players confronted by Bastia fans in ugly scenes.
Stewards and security staff rushed to intervene and for a few minutes there was chaos and scuffles until the playing surface was cleared and the Lyon players took refuge behind a metal gate in the tunnel.
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Lyon initially refused to leave the changing rooms again, but eventually did so to warm up for a second time and the game kicked off soon after with stewards lined up on the edge of the pitch.
However they were powerless to prevent more disturbances at the half-time whistle, triggered by a confrontation between a Bastia official and Lyon goalkeeper Anthony Lopes, who had to be restrained by security men and appeared to be the chief target of the Bastia mob.
Lyon's players huddled in the dressing room and later left the stadium in their team bus after riot police dispersed about 100 waiting Bastia fans massed at the gates by firing tear gas.
The French league's disciplinary commission is certain to hit Bastia hard after it docked them one point -- suspended -- and ordered the club to close its East Stand for three games over the monkey chants by some of its fans at Balotelli.
Nathalie Boy de la Tour, president of the LFP, told AFP: "We regret that Bastia is giving a horrible image of our football, it hurts the image of professional football, which does not deserve this."
On Thursday fans streamed onto the pitch in Lyon's Europa League home clash with Besiktas and the start of the quarter- final first leg was delayed by 45 minutes as officials attempted to clear their Parc OL playing area of fans.