The home team, leading 1-0 in the rubber, once again fell back on their spin force to dismiss opener Stiaan van Zyl for a duck and Imran Tahir (4), who came in as a nightwatchman, before the visitors ended the day at 11 for two after 9 overs at the VCA ground at Jamtha.
Openers Dean Elgar (7) and captain Hashim Amla (0) were at the crease to face Indian spinners Ravichandran Ashwin and Ravindra Jadeja, who tasted early blood by plucking a wicket apiece to threaten mayhem on a spinning track tomorrow.
This is the third time that India have been dismissed in the vicinity of 200 in the series, having fallen for 201 and 200 in the opening Test they won at Mohali to take a 1-0 lead.
In-form opener Murali Vijay top scored with an innings of 40, while wicketkeeper batsman Wriddhiman Saha (32) and Ravindra Jadeja (34) revived the tottering innings briefly. Cheteshwar Pujara (21) and skipper Virat Kohli (22) got decent starts only to throw them away.
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Off spinner Simon Harmer, dropped from the team in the drawn Bengaluru Test after playing in the series opener at Mohali, supported him with a fine haul of 4 for 78, by getting good purchase off the turning track.
Young fast bowler Kagiso Rabada and spinners Elgar and Tahir accounted for the other wickets.
The Indian innings got off to a fine start when Vijay, who struck a six and 3 fours in his 84-ball knock, and Dhawan (12) put on their second successive half century stand of the series.
An opening stand on 50 runs set the innings in the morning before losing Vijay and Dhawan in the second hour to adjourn to the interval at 85 for 2.
Dhawan, denied strike for long, was lured out by Elgar soon after the 50 was raised in 13.4 overs and spooned a drive back to the left arm slow bowler who accepted a return catch to his right.
South Africa, then, hit back strongly through Morkel in the first hour post lunch.
The loss of both the batsmen in the second hour before lunch followed by a dramatic post-lunch middle-order collapse undid the initial good work.
The batsmen dismissed, mostly to poor shots, were Pujara (21), skipper Virat Kohli (22), Ajinkya Rahane (13) and Rohit Sharma, who did not play in the first two Tests.
Samuels raced on quickly thereafter and looked more
comfortable at the crease as time passed, as did Chandrika at the other end.
About 40 minutes were left for lunch when rain intervened and cut short the session. Despite the shower passing by, the umpires called for an early lunch to allow for the ground staff to prepare the field for resumption.
Meanwhile Ashwin, who recorded his 17th five-wicket haul in Tests, ran through the West Indies batting line-up after Samuels and Chandrika defied India in the first session.
The opener's dismissal was followed by those of Jermaine Blackwood, who had a pair in the match, Samuels, debutant Roston Chase, Shane Dowrich and skipper Jason Holder as West Indies slumped to 132 for eight.