Ellis suffered the injury after bowling four overs in the second ODI at the Wanderers on Sunday and will return home with his fitness to be assessed ahead of the home ODI series against England that starts in November.
The tourists will also not be able to call on the services of uncapped left-arm spinner Joel Davies, after he picked up a hamstring strain while fielding as a substitute.
Ellis' injury leaves Australia with just four fast bowlers to choose from for the third and final ODI series, which has already been lost after Proteas won both previous contests, in Potchefstroom.
Pat Cummins is likely to return to the starting XI having not played yet on tour, while Mitchell Starc is also set to take his place back having started the first ODI in Durban and then being rotated out in Johannesburg.
Josh Hazlewood will likely be rested after playing the first two ODIs, with the three-match Test series in mind, with Xavier Bartlett likely to retain his place for the final ODI.
Australia have not yet taken a decision on whether Josh Inglis will return for the Test series which starts on 9 October, after the wicketkeeper-batter fractured his right index finger in the opening ODI.
David Miller produced a career-best innings and Temba Bavuma added a century while the spinners dominated for the Proteas as they secured a second consecutive victory over Australia, winning the second ODI by 32 runs at the Wanderers in Johannesburg.
Australia wicketkeeper Josh Inglis has been ruled out of the remaining two ODIs in South Africa, and is doubt for the Test series that will follow, due to a fractured right index finger.
South Africa recovered from a difficult start to defeat Australia by 67 runs in the first ODI in Durban, taking an early lead in the three-match series.
Australia have called up uncapped allrounder Jack Edwards to their ODI squad for the three-match series against the Proteas, that starts in Durban on Thursday, following an injury to fast bowler Billy Stanlake.
