On Friday, FFA sensationally barred Glory from contesting the 2014-2015 A-League finals - and fined it $269,000 - after it deemed the club to have breached the salary cap, over three seasons.
Perth were set to seek an injunction against its exclusion in the Supreme Court, but, according to a club statement released on Monday, that action has been suspended "in the spirit of the game".
"Perth Glory FC can confirm it will appeal against the Football Federation of Australia's determination and associated penalties," the club statement read.
"The club will exercise its right to appeal via the Federation's Disciplinary Committee.
"Perth Glory has until Tuesday, 21 April 2015, to lodge its appeal.
"The Supreme Court action which commenced last week has been suspended, in the spirit of the game, to allow the FFA appeal process to be exhausted.
Perth deliberately failed to disclose payments and benefits to at least six players, FFA said, adding the club was about $400,000 over the $2.55 million salary cap this season alone.
A statement released by FFA outlined Glory's ladder position - third on 44 points after 25 rounds of the regular season - will be altered to seventh, ruling Kenny Lowe's club out of contention for an AFC Champions League (ACL) place and the right to contest the Premiers' Plate and Championship.
A determined Glory immediately vowed to fight the ruling, with the club filing an injunction with the Supreme Court of Western Australia.
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