England won 3-0 at Derby's Pride Park, but the friendly was overshadowed by Agyemang's knee injury as she was carried off the field on a stretcher.
Agyemang had joined Brighton & Hove Albion on loan for the 2025/26 season.
"We can confirm that Michelle Agyemang suffered a ruptured anterior cruciate ligament injury while playing in England's 3-0 win over Australia in Derby on Tuesday," Arsenal said in a statement.
"The 19-year-old forward... will miss the remainder of the 2025/26 season as a result of the injury. We are in close contact with Brighton as we determine a treatment and recovery programme for Michelle."
England's Football Association said she would also have their full support as she starts her rehabilitation.
"Disappointed that results show a torn ACL," Agyemang wrote on Instagram.
"Recovery starts now, I will be back stronger than before."