Kallis suffered a hamstring injury in Adelaide, having started the match well with the wickets of Ed Cowan and Ricky Ponting.
He left the field and, having been sent for an MRI scan, has been told he will only be allowed to bat for the next four days.
His fitness for the final game in Perth on November 30 has yet to be determined.
Proteas team manager Dr Mohammed Moosajee said: "Jacques has suffered a Grade 1 strain to his right hamstring. He will not be able to bowl in the current Test match but can bat, we can only make a call on his availability for the next Test match closer to the time as it is subject to how he responds to treatment."
Paceman Vernon Philander was ruled out of the game with back trouble before the toss and could return to the side for the third Test.
"Vernon's scan reveals nothing more than a lower lumbar muscle strain as initially suspected," added Moosajee.
"He will receive treatment and undergo rehabilitation during the course of the current Test match and we are hopeful he will be fit for the final Test in Perth."