FFA found that Glory had "deliberately failed to disclose" 400,000 Australian dollars worth of benefits and payments to six players this season, meaning the club will be relegated to seventh spot at the end of the campaign - outside of the finals places.
Perth have pledged to fight the sanction, but showed little resolve on the field as - having seen leaders Melbourne Victory stunned by Newcastle Jets - they succumbed to a Sydney side who now sit above them.
Alex Brosque netted twice - although striker Jamie Maclaren had what appeared to be a legitimate leveller ruled out for offside a minute after the opener - and Bernie Ibini scored a stunner to move Sydney onto 44 points, alongside both Glory and Victory.
In Friday's other fixture, Edson Montano's goal earned the Jets three points at AAMI Park to move Phil Stubbins' side above Western Sydney Wanderers at the bottom of the division.
