The FFA found Perth "deliberately failed to disclose" 400,000 Australian dollars worth of benefits and payments to six players this season.
When the 27 rounds of the A-League regular season are completed, the Glory will be relegated to seventh - outside the top-six positions required to compete in the finals.
Perth have topped the A-League standings for the majority of the season and currently sit second, only behind leaders Melbourne Victory on goal difference.
The Glory have also been fined $269,000 for breaching the salary cap for the past two seasons and the 2014-15 campaign.
The fine was based on the amounts paid over the cap in the past two seasons - $26,000 and 43,000 - plus $200,000 for Perth's infraction this term.
Perth have seven days to appeal.
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