Spin duo Ravindra Jadeja (4-50) and Ravichandran Ashwin (4-70) spun a web around South Africa, who were bundled out for 214 in their first innings on a track that contained no demons.
In reply, India cruised to 80 for no loss with Shikhar Dhawan (45) and Murali Vijay (28) looking largely at ease against South Africa's depleted pace attack.
Vijay got a reprieve on 21, though, when Imran Tahir spilled a simple catch off Morne Morkel's bowling at square leg.
The hosts, who lead the four-match series 1-0, would be particularly happy with Dhawan's return to form after the southpaw scored a duck in both innings of the first test.
Earlier, South Africa crossed the 200-mark for the first time in the series before being all out for a below-par total with de Villiers exhibiting the kind of decisive footwork that was missing from his team mates.
Playing in the city he represents in the Indian Premier League Twenty20 competition, each of the 11 boundaries and the six de Villiers hit was heartily applauded by the large crowd who chanted "ABD, ABD" throughout his knock.
BIGGEST BLOW
The early moisture in the wicket prompted Virat Kohli to opt to field and the India captain introduced Ashwin after seven quiet overs which immediately paid off.
The spinner trapped Stiaan van Zyl plumb in front and, three balls later, had Faf du Plessis caught at short leg as South Africa slumped to 15 for two.
Dean Elgar (38) refused to let Ashwin dictate terms and stepped out to hit the bowler over his head for a towering six before his team suffered another setback.
Varun Aaron had watched all-rounder Stuart Binny pip him to the new ball and the speedster responded by castling rival captain Hashim Amla with the final delivery of his second over.
Elgar perished in the first over after lunch, JP Duminy (15) could not shine on his return to the squad and Dane Vilas (15) fell to a soft dismissal to compound South Africa's crisis after lunch.
Jadeja then dealt the biggest blow in the final delivery before the tea break when wicketkeeper Wriddhiman Saha took a diving, one-handed catch to send back de Villiers.
With Dale Steyn and Vernon Philander both out injured, South Africa's pace attack lacked the usual sting. The visitors also dropped off-spinner Simon Harmer, bringing in a fit-again Morkel, fellow paceman Kyle Abbott and all-rounder Duminy.
(Reporting by Amlan Chakraborty in New Delhi,; editing by Patrick Johnston)
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