Clarke missed most of Australia's triangular one-day tournament with Zimbabwe and South Africa in August and September and all of the team's one-day series against Pakistan in the United Arab Emirates after injuring the hamstring.
The 33-year-old was dismissed for 11 by South Africa paceman Dale Steyn in the first one-day match against South Africa in Perth on Friday and Cricket Australia tweeted the injury news not long after.
"Clarke will (sic) is currently being assessed and will have a scan tomorrow. George Bailey will step up as captain," CA said on its Twitter feed.
The recurrence of the injury almost certainly rules Clarke out of Sunday's second match in Perth and will more than likely keep him sidelined for further matches in Canberra (Nov. 19), Melbourne (Nov. 21) and Sydney (Nov. 23).
Depending on the severity of the injury, Clarke may also be in doubt for the start of the four-Test series against India, which kicks off with the first match in Brisbane on Dec. 4.
Image: Michael Clarke
Photograph: Shaun Roy/Reuters
Cricket Buzz: Gayle returns to Windies squad for South Africa tour
Australia's Haddin in race to be fit for India Test
Feast for fans of raw pace as Australia host South Africa
World Cup pitches will not be conducive to spin bowling, says Hussey
ICC ODI rankings: Kohli, Dhawan among top five, Dhoni down a rung