Kallis anchored the innings with his 81 not out after the home team was put into bat in the series decider under heavy cloud cover at Newlands.
The hosts slipped to 34-2 before Kallis shared half-century partnerships with Hashim Amla (59) and AB de Villiers (26), and an unbeaten stand of 68 with Ashwell Prince (28 not out).
Top-ranked India had troubled South Africa's batsmen on a seaming, swinging pitch as Zaheer Khan and Ishant Sharma struck early.
Shanthakumaran Sreesanth had 2-70 on an opening day when play was interrupted twice by rain.