Siraj struck early to peg South Africa back in their second innings on the second day.
Shubman Gill (90) and Jalaj Saxena (61*) made crucial contributions in the first innings, as India A edged closer to sealing the four-day game versus South Africa A in Thiruvananthapuram. At stumps on Day 2, the visitors were in deep trouble at 125 for 5 in their second dig, still needing 14 runs to make India A bat again.
After bowling India A out for 303 in their first innings, the visitors would have hoped to put on a better show the second time around. However, Thakur and Mohammad Siraj once again made early inroads by picking up the scalps of Aiden Markram and Pieter Malan to leave the tourists reeling at 14 for 2.
Shahbaz Nadeem then joined in the act by removing Khaya Zondo and Senuran Muthusamy. With South Africa A in desperate need of a partnership of some substance, Zubayr Hamza (44) and Heinrich Klaasen (35*) shared a stand of 42. Unfortunately for the visitors, Hamza fell to K Gowtham as South Africa A slid further. Klaasen and Wiaan Mulder then guided the side to close of play.
Earlier, Gill, the India A skipper, had powered his side past South Africa's A first-innings total before falling to Dane Piedt. Gill's wicket opened the floodgates for South Africa A to make a comeback. The duo of Lungi Ngidi and Lutho Sipamla combined to run through the middle and lower order, with the home side slipping to 199 for 7.
At that juncture, Thakur (34) and Jalaj shared a vital alliance of 100 to ensure India A wouldn't lose control of the game. Ngidi dismissed Thakur while Piedt snared the last two wickets to fall to clean up the tail. Meanwhile, Jalaj remained undefeated.
Brief scores: South Africa A 164 (Marco Jansen 45*; Shardul Thakur 3-29, K Gowtham 3-64) and 125/5 (Zubayr Hamza 44; Shahbaz Nadeem 2-13) trail India A 303 (Shubman Gill 90, Jalaj Saxena 61*; Lungi Ngidi 3-50) by 14 runs.