Pant, who did not play a Test in this series, came on to replace him.
"Wriddhiman Saha has been replaced by Rishabh Pant who has taken a blow right on the end of the gloves," a BCCI tweet said.
Saha has been brilliant in this series behind the stumps, especially in the second Test in Pune where he took a couple of excellent catches. The Bengal stumper has previously been out of the team due to a long injury layoff.
The visitors are on the brink of another embarrasing defeat as they got bowled out for a mere 162 in their first innings in reply to India's 497/9 declared. In the second innings, Proteas are again in trouble having lost six wickets when the story was being written.