The star batter has endured a roller coaster series, suffering a broken jaw on the eve of the one-off Test, but still managing to play a crucial role in the drawn thriller in Canberra.
Mooney then scored a match-winning 73 in Thursday's first ODI, but left the field early after experiencing quadricep tightness.
Teenage quick Darcie Brown, who skittled England with 4-34 three days ago, also misses out with Ashes secured and a World Cup campaign looming.
Nicola Carey and Annabel Sutherland have been brought back into the team, with Australia to bowl first after captain Meg Lanning won the toss.
England have made just the one change, with Charlie Dean coming in for Katherine Brunt.
Australia: Alyssa Healy, Rachael Haynes, Meg Lanning (capt), Ellyse Perry, Tahlia McGrath, Ashleigh Gardner, Annabel Sutherland, Nicola Carey, Jess Jonassen, Alana King, Megan Schutt.
England: Tammy Beaumont, Lauren Winfield-Hill, Heather Knight (capt), Nat Sciver, Amy Jones, Sophia Dunkley, Danni Wyatt, Charlie Dean, Sophie Ecclestone, Anya Shrubsole, Kate Cross.
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