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Cummins took six wickets in three tour matches against Zimbabwe, South Africa A and India A over the past month, but CA said he would return early to have his injury treated.
"Pat reported some left rib/back pain during the Australia A game against India A last week," team physiotherapist Kevin Sims said in a statement.
"With only Wednesday's final remaining in the series, the decision was made for him to return to Australia to assess the injury."
It is a worrying sign for the rising 20-year-old paceman, who has missed the last two Australian domestic summers with back and foot injuries following a remarkable Test debut in 2011.
Cummins claimed man-of-the-match honours against South Africa in Johannesburg, which included claiming 6-79 in the second innings and hitting the winning runs in a narrow Australian victory.
He was also sent home from Australia's one-day tour of England in the middle of last year with a side strain.
Cummins has made just six first-class appearances in three years due to his long list of injuries. and had returned home for assessment.
