A statement from Cricket South Africa said the paceman was sent for scan which determined the extent of the injury and he will remain in Australia with the medical team to undergo rehabilitation.
Kwena Maphaka, who was the highest wicket-taker with nine scalps in the T20I series, will remain with the Proteas squad as fast bowling cover.
Rabada was rested for the tour to Zimbabwe in July and returned to the national side for the recently concluded three-match T20I series in Australia that the Proteas lost 2-1.
The 50-over series started in Cairns on Tuesday with the visitors giving batter Dewald Brevis and spinner Prenelan Subrayen debuts in the ODI format.
Brevis was the star of the show in the last two T20I matches, hitting a century and fifty to announce himself on the international stage.
Lungi Ngidi and Nandre Burger were the two specialists fast bowlers selected with seam-bowling allrounder Wiaan Mulder and left-arm spinner Keshav Maharaj also in the starting line-up.
Temba Bavuma returns from a hamstring strain to captain the Proteas and will bat at number three with Aiden Markram and Ryan Rickelton set to open innings.
Keshav Maharaj took a maiden five-wicket haul to help the Proteas canter to a 98-run victory against Australia in the first game of the three-match ODI series in Cairns on Tuesday.
Proteas captain Temba Bavuma has confirmed he will shift down the order and bat at number three in the three-match ODI series against Australia, starting in Cairns on Tuesday.
Glenn Maxwell struck a brilliant unbeaten 62 off 36 balls to help Australia beat South Africa by two wickets with one ball to spare in the third and final T20I in Cairns and seal the series 2-1.
Captain Aiden Markram says his move to the top of the order in the Proteas' T20I batting line-up was to accommodate "more destructive" players in the middle-order.
