Kallis, who strained his right hamstring early on day one, struck 58 to help South Africa avoid the follow-on on day three of the second test, but was in obvious pain as Australia's pacemen targeted the bulky all-rounder with short-pitched bowling.
"We knew he would always be able to bat. The challenge was what's going to happen when he runs," Mohammed Moosajee told reporters at Adelaide Oval.
"So it's safe to say he's probably aggravated his injury by running and batting. He's still probably going to have to bat the second innings.
"If that happens there's no guarantee to be fit and ready for the next test, with the three-day turnaround.
"Cricket South Africa's selection committee back home are looking into possibly sending out someone as cover but they haven't made a decision as yet."
Kallis's loss would be a major blow for the tourists, who face an uphill battle to defeat Australia in the second test.
Kallis, who was ruled out of bowling duties on day one, winced repeatedly as he ducked to avoid bouncers launched by Peter Siddle and the Australian pacemen on Saturday.
After being dismissed for 388, South Africa rattled through Australia's top order to leave the hosts on 111-5 at the close, leading by 273 runs.
The 37-year-old Kallis scored 149 and 49 in the drawn first test in Brisbane.
Australia and South Africa start the third test in Perth on November 30.
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