Home fans at the Armand Cesari stadium targeted Lyon's players as they warmed up before the game, delaying the start by nearly an hour. There was more disruption 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. "We're not going to war."
Bastia, who were bottom of the league going into the match, 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.
The French professional football league (LFP) said in a statement: "Following the new incident at the end of the first period, the LFP decided to definitively stop the game between Bastia and Lyon."
In the first incident, Lyon players fled to the dressing rooms and the kick-off was postponed as team captains and league officials discussed whether the game should go ahead.
Lyon's players had been finishing their pre-game warm-up when about 50 Bastia fans attacked them. The trouble started with a Bastia fan who came out from behind the goal where Lyon were practising and kicked a ball.
That sparked an exchange with Lyon players and more Bastia supporters from behind the goal quickly streamed onto the pitch. Lyon striker Memphis Depay was among the Lyon players pushed by Bastia fans. Stewards and security staff intervened and there were scuffles with fans until the playing area was cleared.
Initially Lyon’s players refused to leave the changing rooms again. However they were eventually persuaded to do so and following another warm up, the game kicked off with stewards lined up on the edge of the pitch.
However stewards 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 fans.
The French league's disciplinary commission is likely to punish Bastia 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.