The last-wicket pair of Lutho Simpala and Lungi Ngidi were at the crease when bad light stopped play.
Jalaj Saxena, whose unbeaten 61 helped India A open up a 139-run first innings lead, starred with the ball too picking up two of the four wickets to fall in the day.
Shahbaz Nadeem removed Dane Piedt to snare his third scalp in the innings, while the other wicket, that of Wiaan Mulder for 46, the first of the day - came due to a direct hit from Ricky Bhui.
For the tourists, Heinrich Klaasen was the top scorer with 48.
Brief Scores South Africa A 164 iamp; 179/9 (Heinrich Klaasen 48; Shahbaz Nadeem 3/17) vs India 'A' 303 (Shubman Gill 90, Jalaj Saxena 61*; Lungi Ngidi 3/50)