The 38-year-old - playing in his final Test for the Proteas - received a guard of honour on his way onto the pitch and will resume on 78 not out on Sunday, as rain and bad light brought a premature end to proceedings in the decisive Test at Kingsmead, Durban.
South Africa reached 299-5 at stumps, with AB de Villiers' 74 and Alviro Petersen's 62 aiding the hosts' cause, while Ravindra Jadeja was the pick of the bowlers, as his skill and precision resulted in four wickets on Saturday.
Resuming play on 82-0, South Africa made steady progress before Graeme Smith (47) tried to slog Jadeja over mid-on, but succeeded only in picking out Shikhar Dhawan at midwicket - who took a amgnificent catch over his shoulder.
Hashim Amla (3) was soon clean bowled by Mohammed Shami, while from the very next delivery, Petersen edged Jadeja to Murali Vijay at slip, leaving South Africa on 113-3.
The partnership between De Villiers and Kallis steadied the South Africa innings, with the duo regularly finding the boundary.
But India broke the 127-run stand before tea, as the brilliant Jadeja tempted De Villiers into a loose drive, and he presented a simple catch for Virat Kohli at first slip.
Still trailing by 94 runs, South Africa's run rate dried up as they employed a more defensive stance.
JP Duminy (28) faced 82 deliveries, before he was trapped lbw by Jadeja.
Shortly after a combination of rain and bad light brought a halt to proceedings and, with further forecasts of rain over the next two days, there remains little time for either side to claim victory, with South Africa looking to score quick runs on Sunday with Dale Steyn partnering Kallis at the crease.