The club have already served one match of the ban when they beat basement side Nancy in Gueugnon, eastern France, last month after they were banned from using their own ground pending the ruling.
Promoted Bastia, 13th in the league, will now have to play their next two home matches, against Stade Rennes and Evian Thonon Gaillard, at a neutral venue.
They were also fined 30,000 euros.
A two-game ban and the suspended deduction were imposed after a linesman was hit by a missile during the home League Cup quarter-final against Lille in November, the LFP said on their website on Friday.
The Corsican club were barred from playing at home for a further game after fans threw fireworks outside the Furiani stadium as Bastia's 2-1 league defeat by Olympique Marseille was played behind closed doors.
The stands were empty for the encounter against Marseille after ugly incidents marred the game at neighbours Ajaccio in October.
Bastia visit 15th-placed Stade Reims on Sunday.
