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.
Younousse Sankhare's victor in the 65th minute lifted the visitors to fifth place with five matches left to play.
The game, as it stands, is under threat of being called off with OL players refusing to return to the pitch.
Lyon players have been attacked on the pitch by supporters of Bastia, leading to the Ligue 1 game being delayed for nearly an hour.
Alexander Lacazette, Lyon's top goalscorer, was not in the squad but tweeted: "Pffff shameful!" However, after further chaos at half-time, the league's authoritative body, the LFP, has chose to put a stop to the game.
"Following the new incident at the end of the first period, the LFP made a decision to definitively stop the game between Bastia and Lyon", the French professional football league (LFP) said in a statement. "The LFP condemns in the strongest possible terms the incidents which occurred before the match and at half-time of the match SC Bastia / Olympique Lyonnais".
"The players have quickly huddled together, they and the staff are very shocked. The moment it happened, none of us wanted to come out of the dressing room and play this match".
L'Equipe journalist Vincent Duluc was quoted on the OLTV account as saying: "Memphis was pushed by a supporter".
There was little action of note in the 45 minutes played, with Lyon dominating possession but failing to trouble Jean-Louis Leca in the Bastia goal. Lyon is facing likely sanctions from UEFA after crowd disorder delayed its Europa League home quarterfinal against Besiktas midweek.