Chinaman bowler Kuldeep Yadav (2/51) and left-arm spinner Shahbaz Nadeem (2/41) took two wickets each as Proteas skipper Aiden Markram waged a lone battle to remain unbeaten on 83 from 140 balls, his innings laced with 12 fours.
At close of play, Wiaan Mulder was at the crease with him on 9. Apart from Markram, only Theunis de Bruyn (41) got runs as the other batsmen fell prey to Kuldeep and Nadeem's guile.
Pacer Mohammed Siraj also snared one wicket.
Earlier, India 'A' rode half centuries from Shivam Dube (68 off 84 balls; 10/x4, 1x6) and Wriddhiman Saha (60 off 126 balls; 8x4) to post a challenging 417 in their first innings.
Resuming on 233/3, Saha added to his overnight tally of 34 while Karun Nair got out on Day 1's score of 78.
Dube also played a brisk innings where he hit the bowlers all over the park to up the ante. At the end, Jalaj Saxena remained unbeaten on 48 to help India 'A' go past the 400-run mark.
For South Africa 'A', Wiaan Mulder (3/47) and Dane Piedt (3/78) were the best bowlers.
Brief Scores: India 'A': 417 all out (Shubman Gill 92, Karun Nair 78, Shivam Dube 68, Wridhhiman Saha 60; Wiaan Mulder 3/47, Dane Piedt 3/78); South Africa 'A': 159/5 (Aiden Markram 83 batting; Shahbaz Nadeem 2/41, Kuldeep Yadav 2/51)