Lyon striker Alexandre Lacazette, who was rested for the game, took to Twitter to express his anger.
Lyon initially refused to play the game after the incident, but after lengthy negotiations the game went ahead 52 minutes later than it was first scheduled to.
As the pre-game warm-ups were coming to an end, some Bastia supporters invaded the pitch and tried to attack Lyon's Memphis Depay.
Lyon players, including goalkeeper Mathieu Gorgelin, are attacked on the pitch.
A security staff holds Lyon's goalkeeper Anthony Lopes (C) during scuffles at half-time between some of Lyon's players and Bastia supporters who invaded the pitch, during the French L1 football match Bastia (SCB) vs Lyon (OL) on April 16, 2017 in the Armand Cesari stadium in Bastia on the French Mediterranean island of Corsica.
"Following the new incident at the end of the first period, the LFP made a decision to stop SC Bastia / Olympique Lyonnais", the statement said.
"The LFP condemns in the strongest possible terms the incidents that took place both before the SC Bastia/Olympique Lyon match, and during halftime", it said in a statement.
According to Lyon's club TV channel, the players were told to return to the dressing room after boarding the team bus as local officials couldn't guarantee their safety on exit.
"The players all huddled together". Lots of them had been throwing balls at the players and they just started pushing them and then a fight broke out.
It has to be said that many Bastia supporters jeered the pitch invaders as they were against their actions. "I've never seen anything like it in 30 years".