Fowler withdrew from interim Matildas boss Tom Sermanni's extended squad on Sunday, just days after World Cup hero Cortnee Vine made herself unavailable for similar reasons.
The Matildas will also be without Katrina Gorry (shoulder) and Clare Wheeler (leg) after the midfielders suffered injuries playing for their clubs.
A replacement for Fowler has yet to be made, with the first of four matches in the international window to be played against Brazil in Brisbane on Thursday night.
Manchester City forward Fowler, who looms as the future of the Matildas' attack, will instead spend November and December in Australia with family.
"I've decided to take this time to prioritise recovery in order to refresh both mentally and physically, so that I can continue to put my best self forward for both club and country," Fowler said in a Football Australia statement.
"Playing for the national team is something that I never take for granted.
"I have, however, through past experiences, come to realise that my mind and my body are also things that I should also never take for granted.
"I really appreciate everyone's support and understanding, and I hope to see you all soon."
📰 SQUAD UPDATE: Football Australia has announced extended squad updates ahead of the commencement of the upcoming November / December FIFA Women's International Window.— CommBank Matildas (@TheMatildas) November 24, 2024 #Matildas
Sermanni could also be without A-League Women midfielders Isabel Gomez and Hana Lowry after the duo suffered injuries in their respective club matches.
Central Coast player Gomez is yet to discover the extent of her right leg injury after a collision in their draw with Melbourne Victory on Saturday, while Sydney FC's Lowry suffered a knee injury just hours before Fowler withdrew from the squad.
Sermanni will at least have Natasha Prior for selection after the Newcastle Jets defender was cleared of a serious ankle injury to join the Matildas training camp.
Veteran striker Michelle Heyman sent a scare through the Canberra United and Matildas camps after she appeared to suffer an injury in the ALW match against Perth Glory.
The midfielder clutched her ankle immediately following a contest in front of Glory's goal but was able to return to the game.
Australia will play Brazil at Suncorp Stadium on Thursday and at Cbus Super Stadium on December 1, and meet Taiwan in Victoria on December 4 and 7.
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