An extensive audit into the Glory's finances by Football Federation Australia (FFA) last week resulted in the governing body deeming the club to have systematically breached the cap throughout the last three seasons and by more than AU$400,000 this term alone.
Perth have subsequently been fined $269,000 and barred from the 2014-15 play-offs.
Glory, who led the league for much of the campaign and had been firmly in contention to win the Premier's Plate, will be deemed to have finished seventh at the end of the regular season.
"I would like to personally apologise for a series of events which have resulted in the club facing sanctions by the Football Federation of Australia," Brewer said in a statement released on Thursday.
"As CEO, I ultimately take full responsibility for these actions which have resulted in the club being eliminated from this year's A-League finals campaign."
Despite quitting over his role in the scandal, Brewer continued to the protest the veracity of FFA's findings.
Perth have appealed to the governing body's disciplinary committee and have also considered seeking a Supreme Court injunction against their exclusion from the finals.
"There have been no so called 'secret' or 'third-party' payments made on behalf of the club," Brewer added.
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