Basement club Montpellier were 2-0 down to their relegation rivals, with Lucas Stassin netting twice, his second coming eight minutes after the break which enraged the home support.
Flares landed on the pitch and the referee stopped play for three minutes before the match resumed, but supporters then began moving back from the front of the stand as smoke and flames could be seen in their sector.
The referee sent the players back to the dressing rooms and after a 20-minute suspension an announcement was made informing the fans that the match had been abandoned.
Montpellier supporters caused a match to be abandoned in October 2023 after Clermont's goalkeeper was targeted by a firecracker.
Montpellier have lost their last six league games, winning only four all season, and are in 18th place on 15 points after 25 matches, six adrift of the relegation playoff spot. Saint-Etienne sit one place higher on 20 points.