The 5-4 penalty shootout defeat to Auxerre in May was followed by ugly scenes, with supporters clashing with police and security staff after storming the pitch and targeting players.
The Ligue de Football Professionnel announced on Thursday that the club had been handed a six-point deduction, though three were suspended.
Saint-Etienne will also play its first four home games of the season at an empty Stade Geoffroy-Guichard after two of the six-match ban they received were suspended.
The club said in a statement: "Given the nature of the facts, Saint-Etienne has decided not to appeal the decision.
"The club appeals strongly to everyone's responsibility so that these unspeakable acts never happen again at the Geoffroy-Guichard."