In making his announcement, Brewer - who took on the job almost two years ago - apologised for the administrative errors that led to the club being sanctioned for salary cap breaches over the past three seasons.
The development came just a day after Football Federation Australia announced it is poised to issue the beleaguered club with a third show cause notice for the alleged 'failure to disclose reportable benefits and payments in excess of $100,000' - for the 2014-2015 season.
Glory, which sits third in the A-League, will have its ladder position altered to seventh at the conclusion of the campaign and has been fined $269,000.
More on the Perth Glory salary cap saga
Perth Glory kicked out of A-League finals for breaching the salary cap
"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," a statement released by Brewer read.
"As CEO I ultimately take full responsibility for these actions which have resulted in the club being eliminated from this year's Hyundai A-League finals campaign.
"The decision by the FFA to eliminate the club from the finals, in no way reflects the massive effort undertaken this year by everyone, involved with the club.
"I would like to stress that I genuinely love Perth Glory FC and all those involved with the club.
"Two years ago I stepped into the role with the belief that I could make a difference.
"As a father of three, I have always wanted the best for my family and I applied the same principal to my "football" family and have at all times wanted the best for the club, its staff, sponsors, players, members and supporters.
"There has been much media speculation regarding the club's salary cap position.
"Like every A-League club, we manage it throughout the season and it must be made very clear that this club has made each and every payment through its own records.
"There have been no so called "secret" or "third party" payments made on behalf of the club.
"I unreservedly apologise to the staff, sponsors, members, fans and players of Perth Glory for the position in which the club finds itself in."
Brewer urged fans to attend Glory's Round 26 match against Melbourne City at nib Stadium as the spectre of more FFA sanctions looms large.