Harmer bowled a fine line to dismiss Ajinkya Rahane, Ravindra Jadeja and Amit Mishra as India lost 6 wickets after resuming at 125-2.
India got through the first hour steadily before the world's top-ranked test side got the first breakthrough when part-time seamer Stiaan van Zyl removed captain Virat Kohli caught behind, and then leg-spinner Imran Tahir dismissed the other overnight batsman Cheteshwar Perera for 77.
Four more wickets followed in quick succession.
At the break, Wriddhiman Saha was eight not out.
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