Clarke pulled up sharply while fielding and left the field with the team physiotherapist.
Clarke needed to pass a fitness test on recurring hamstring troubles before playing in the Adelaide Test, but looked as if he was well on the mend after scoring 128 in the first innings and fielding during both Indian innings.
He has a history of chronic lower back issues and a related hamstring injury and there are now doubts he will be fit to play in next week's second Test in Brisbane, given the short turnaround in Test matches.