The Gujarat Giants captain's brief participation in the inaugural Women's Premier League (WPL) came to an end on Thursday due to a calf injury, rendering her ineligible for the remainder of the competition.
After Mooney suffered the injury in Gujarat's first T20 league game last weekend, it will take up to six weeks for her calf to heal.
The 29-year-old will now travel home to undergo rehabilitation, and South African Laura Wolvaardt will take her place in the Gujarat squad.
Her team Super Women has released Wolvaardt, who was in Pakistan for the Women's League exhibition matches.
Mooney made the following statement: "I was really looking forward to the first WPL season... unfortunately injuries are part and parcel of the sport, and I am gutted to be missing the remainder of the season."
She said of Gujarat, who are fourth in the five-team league with one win and two losses: "I will be keeping a close eye on the team's performance from afar and will be rooting for them every single day." Gujarat has one win and two losses.
"I am looking forward to coming back stronger, fitter, and I will definitely be hungrier next season," despite the fact that I will be absent from the field for the remainder of the season.
Mooney, one of the three Australians to skipper groups in the principal WPL season, top-scored for Australia in their triumph in the last of the T20 World Cup against South Africa in February.
Meg Lanning and Alyssa Healy, two of Mooney's fellow Australians, are in charge of the Delhi Capitals and UP Warriorz, respectively.