Play was possible in the middle session where India A dominated the proceedings as they bagged four wickets, out of which Rajpoot claimed two.
First Rajpoot removed Dussen for 22 and then claimed the wicket of Second for 47, leaving the visitors at 236 for 5.
Rajpoot had Dussen caught by Srikar Bharat and induced Second to offer a catch to Prithvi Shaw.
At the draw of stumps, Senuran Muthusamy was batting on 23 after facing 63 deliveries.
Yesterday, Yuzuvendra Chahal had claimed two wickets while Siraj had got one.
India had scored 345 all out in their first innings with Hanuma Vihari hitting a century (148 off 295 balls) while Ankit Bawne had contributed 80 from 146 deliveries.
Pacer Duanne Olivier had taken a 6/63 for South Africa A.
India A first innings: 345 all out in 101 Overs (Hanuma Vihari 148; Duanne Olivier 6/63).
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