Ajinkya Rahane remained unbeaten on 100, his second century of the match, having raised a series-high 154-run partnership with skipper Virat Kohli who fell for 88 earlier in the morning.
Wriddhiman Saha was unbeaten on 23 when India declared 30 minutes before the lunch break.
Morne Morkel was the pick of the South African bowlers, claiming 3-51.
South Africa folded for 121 in the first innings and have not scored more than 185 in the spinner-dominated series.
India have already taken an unassailable 2-0 lead in the four-match series.
(Reporting by Amlan Chakraborty in New Delhi; editing by Sudipto Ganguly)
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