Football Australia (FA) confirmed on Tuesday morning Fowler would not feature in the upcoming international window, with four-cap Charlton midfielder Leah Davidson called up in her place.
"Mary Fowler has been withdrawn from the October international window due to personal circumstances," FA said in a statement.Â
"The decision was made following discussions between Fowler, Manchester City and Matildas staff."
Fowler's absence is a blow for coach Joe Montemurro ahead of the two important friendlies.
The 23-year-old has been in terrific form for club Manchester City and likely would have played a key role in both games as Australia's best creative attacking player.
The Matildas are already without star midfielder Kyra Cooney-Cross for this window.
The games against Germany in Karlsruhe on Saturday AEDT and Haiti in Chambly next Wednesday serve as critical preparation for next year's World Cup.
Montemurro has been keen to test his Matildas team against a variety of opponents.
World No.3 Germany are an ominous prospect while world No.47 Haiti have the powers of Ellie Carpenter's former Lyon teammate Melchie Dumornay, one of the best attackers in the world.
Davidson, 25, has been rewarded after making an off-season move from Melbourne City to England's top flight with newly-promoted Charlton.
The midfielder has four caps and one goal since her debut in 2004.
Every player in the squad except Melbourne Victory goalkeeper Courtney Newbon is based overseas.
Newbon, Hana Lowry and Tori Tumeth are the only uncapped players in the squad.
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