The Wanderers' supporters group, known as the Red and Black Bloc (RBB), lit the flares in the first 16 minutes of the match.
The club have until Thursday to respond to the notice, the FFA said.
Wanderers' chief executive John Tsatsimas had earlier said the seating section where the RBB sit -- called the active support area -- would be shut for their match against the Perth Glory on March 4.
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"The Western Sydney Wanderers maintains its position that it will not accept offensive behaviour being displayed at its matches and also will not accept the illegal use of incendiary devices," Tsatsimas said in a statement.
"The majority of those members in the active area have been outstanding and supportive of the club and the team.
"Unfortunately a small group have made this action unavoidable."
Tsatsimas said the club would re-open the area for their match against the Wellington Phoenix on March 10.
"However should there be any further breaches of the terms of admission then the club reserves the right to close down the active area for a further indefinite period," Tsatsimas added.
The Wanderers have had issues with the behaviour of their fans in the past, with the club banning 14 fans after they displayed an offensive banner in their clash with Sydney last February.
The club were also fined A$20,000 (11,233 pounds) by FFA for bringing the game into disrepute.
Fans were warned at the time by Tsatsimas that if there was any further trouble they would shut the seating section down.
They were given a suspended points deduction until the end of last season after fans lit flares in a previous match.
(Writing by Greg Stutchbury in Wellington; Editing by Amlan Chakraborty)
