Five of the six bowlers, employed by Indian captain Cheteshwar Pujara, got at least one wicket each as hosts were still trailing by 376 runs.
Talented JP Duminy (36) and Thami Tsolekile (9) were at the crease at the break.
Ishwar Pandey scalped two wickets in his nine overs, while Mohammed Shami (1/41), Shahbaz Nadeem (1/65) and Suresh Raina (1/25) picked up one wicket each to make life difficult for the South African batsmen.
The pacer had Elgar trapped infront of the wicket as the hosts lost their second wicket at 22.
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Resisting the Indian bowlers well, left-handed batsman Rilee Rossouw scored a 64-ball 57 and shared a 72-run stand for the third wicket with overnight batsman Simon Harmer (22).
Pandey had Harmer caught behind and soon Rossouw joined him in the pavillion when he was trapped by Raina. Temba Bavuma, who joined Duminy at the crease, could not even open his account as he was caught by Raina off Nadeem.
However, Indians broke the 75-run stand when Pandey had Ontong caught behind just before the tea break.