Kallis was not required to bat again as South Africa reached their target of 58 soon after tea to win the series 1-0.
Earlier Ajinkya Rahane was the last wicket to fall in India’s 223, four short of a maiden Test century.
The South Africa players all wore T-shirts featuring an image of Kallis and the words ‘the only player to score 10,000 runs and take 250 wickets’ emblazoned on the back.
They joined the all-rounder for a lap of honour around the Kingsmead outfield, the ground where he made his Test debut against England as a 20-year-old in 1995.
“It’s a very tough day but my team-mates have made it a special game and I couldn’t ask for a better exit,” said Kallis, who will continue to play one-day internationals.
South Africa skipper Graeme Smith said: “We’ve enjoyed time in many changing rooms and had many victories for the Proteas. He’s a really outstanding human being it’s been a privilege to get to know him as a person and a friend. It’s emotional and humbling to see the effect he has had.”
India began the final day 98 runs behind with eight wickets still intact but had the worst possible start when Virat Kohli was given out caught behind from the first ball of the day.
Replays showed the short ball from Dale Steyn clipped Kohli’s shoulder – but with the Indian authorities objecting to the use of the Decision Review System during the series, no review was possible.
There was little doubt about the dismissal of Cheteshwar Pujara in Steyn’s next over, however, a rapid delivery moving off the seam and crashing into the off-stump.
That brought Rahane to the crease in only his third Test, and although wickets continued to fall around him, he reached his second 50 of the match with a single in the final over before lunch.
With nine wickets down, Rahane drove Vernon Philander down the ground to reach 90 and then added a six over point two balls later, before his leg-stump was disturbed with the final ball of the over.
Kallis led the players off the field but there was no change in the batting order as regular openers Smith and Alviro Petersen took less than 12 overs to secure a victory that increases South Africa’s lead over India at the top of the Test rankings.