Lutho Sipamla took 3-63 as India A finished day two of the third four-day match in Bloemfontein on 229-6.
They trailed the hosts by 39 runs after a dominant half-century from Ishan Kishan (86* off 141 balls, 12 fours, one six).
South Africa A began Tuesday on 249-7 after an eventful opening day with Sarel Erwee (75), Tony De Zorzi (58) and Khaya Zondo (56) scoring fifties.
The hosts only managed to add 19 runs to their overnight score following an impressive morning spell from right-arm medium pacer Deepak Chahar.
The 29-year-old took the remaining three wickets to finish with figures of 4-45 as SA A ended on 268 all out.
The visitors also suffered early setbacks in their first innings with the bat, losing four of their five top batters for 92 runs, including the scalp of Abhimanyu Easwaran for 28.
The rebuild was then launched by captain Hanuma Vihari (63 off 170 balls) and wicketkeeper-batter Kishan, with both reaching their half-centuries in a vital 115-run partnership for the fifth wicket.
The stand was eventually ended by Sipamla, who trapped Vihari leg before wicket in the 71st over.
Kishan then expertly guided India A to the end of the day’s play, despite losing Chahar (10) with the last ball before stumps.
SA A’s other wicket-takers were Marco Jansen (1-43), Migael Pretorius (1-27) and Senuran Muthusamy (1-54).
