The two teams tied 2-2 on aggregate after a 1-1 draw in the second leg at St-Etienne’s Gauvreux Gichard, before Aussie beat 5-4 on penalties.
Algerian midfielder Riad Boudebouz was the only one to miss a penalty kick from Saint-Etienne.
French media reported that the police used tear gas canisters to disperse the fans, while the players returned to the dressing rooms after some fans stormed the pitch and threw fireworks from the stands.
Saint-Etienne was forced to play without its fans earlier this month, after fireworks ignited in the stands during their 4-1 loss to Monaco in April, disrupting play for nearly half an hour.
Ausser will replace Saint-Etienne in the first division, accompanied by Toulouse and Ajaccio, while Metz and Bordeaux are also relegated to the second division.