The sanction is in response to crowd behaviour during the Wanderers clash with Melbourne Victory at Etihad stadium on Saturday, where several flares were lit in the active supporter bay.
The three suspended competition points will be deducted if a serious incident occurs that the FFA determines should trigger the suspended sanction and will apply through to 6 February 2017.
“The events of last Saturday night and the coordinated misconduct of a section of Western Sydney Wanderers fans cannot be tolerated by anyone in Australian football,” FFA CEO David Gallop said.
“The misconduct was not only dangerous and threatening but the coordinated and calculated way the fans behaved was a serious blight on the reputation of football and everyone involved in our game including clubs, members, fans, players and officials.
The FFA has also announced it will be formulating a National Flare Management Policy, which will be part of the Fan Banning Process review to be considered by the FFA Board next week.
“The use of flares and associated devices at sporting events are extremely dangerous, illegal and have no place in Australian football,” Gallop said.
“We are putting a line in the sand. If these people are true football fans they will understand and appreciate their actions will hurt the clubs they claim to support.”