Football Federation Australia found the former Asian champions guilty of bringing the game into disrepute after Wanderers fans lit flares and set off detonators during a 1-1 draw at Melbourne Victory.
"The events of last Saturday and the coordinated misconduct of a section of Western Sydney Wanderers fans cannot be tolerated," FFA chief David Gallop said in a statement.
"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."
The FFA can impose the points deduction for any "serious incidents" that might occur over the next 12 months and will be in place through to Feb. 6, 2017.
Western Sydney top the A-League table on 34 points, ahead of Brisbane Roar on goal difference.
"The sanctions have been set taking into consideration the seriousness of the incidents but a clear commitment both publicly and through its submission that the Wanderers will take responsibility for implementing a clear strategy to identify and exclude these individuals," 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."
The passionate support for Western Sydney has been a big part of the story of the rise of a club that went from expansion team to Asian Champions League winners in less than three seasons.
The club backed their fans last year in a row with the FFA over the lack of an appeals process for supporters banned from A-League matches.
Chief executive John Tsatsimas said Wanderers accepted Thursday's punishment, adding that new measures would be put in place to prevent any "further negative impact" on the club.
"We have always been consistent in our stance on anti-social behaviour and use of flares – that is one of zero tolerance," he said.
"We implore all of our members to stand together to ensure we do not receive further sanctions and to assist in fixing this problem for good."
(Reporting by Greg Stutchbury in Wellington; Editing by Nick Mulvenney/Amlan Chakraborty)
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