Australia coach Tom Sermanni had been confident the star striker would be able to return to action for their two-match series on home soil but was overruled by Chelsea.
Sonia Bompastor, coach of the Women's Super League club, had last week ruled out any prospect of Kerr returning to competitive action until mid-April at the earliest after the looming international break.
"Sam's still making a comeback from her knee operation a year and a bit ago," Sermanni said on Monday in Newcastle.
"She's not been fully cleared yet by Chelsea. She's on the mend and she's not too far off.
"Her first priority is to get her on the field at Chelsea and then hopefully she'll be available for selection for the Matildas."
Kerr has not played since tearing an anterior cruciate ligament during the her club's warm weather training camp in Morocco in 2024.
The 31-year-old was hoped to bolster a floundering Matildas side against South Korea, having been sorely missed in their disastrous Olympics and SheBelieves Cup campaigns.
Knocked out in the group stages of the Paris Games, the Matildas left the US in February without a single point.
Australia's national women's team have since slumped to their equal-worst position in the history of FIFA world rankings since they were introduced in 2003, down to No.16.
A-League Women stars Holly McNamara and Michelle Heyman remain in Sermanni's squad as attacking options in Kerr's absence, alongside Mary Fowler and Hayley Raso.
Sermanni has recalled young defenders Courtney Nevin and Jamilla Rankin, while midfielder Clare Wheeler returns after missing out on the last two international windows through injury.
Daniela Galic, Laini Freier and Alana Murphy make way for the new inclusions.
The Matildas begin their path to the 2026 Asian Cup when they play South Korea first at Allianz Stadium on April 4 then at Newcastle's McDonald Jones Stadium on April 7.
The Koreans had condemned Australia to their worst finish at an Asian Cup in 2022, knocking the Matildas out in the quarter-finals.
AUSTRALIA'S 23-PLAYER SQUAD:
Goalkeepers: Mackenzie Arnold, Chloe Lincoln, Teagan Micah
Defenders: Ellie Carpenter, Steph Catley, Charlotte Grant, Winonah Heatley, Clare Hunt, Alanna Kennedy, Courtney Nevin, Natasha Prior, Jamilla Rankin
Midfielders: Kyra Cooney-Cross, Katrina Gorry, Emily Van Egmond, Clare Wheeler, Tameka Yallop
Forwards: Caitlin Foord, Mary Fowler, Michelle Heyman, Holly McNamara, Hayley Raso, Kaitlyn Torpey.
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