Captain Temba Bavuma had won what looked like a crucial toss and opted to bat in the first Test match played at the Barsapara Cricket Stadium in Guwahati.
Aiden Markram and Ryan Rickelton were watchful in some helpful conditions for the India seamers with an earlier start than usual.
The opening batting pair did well to see off Mohammed Siraj and Jasprit Bumrah as scoring became slightly easier once the pitch had settled down and the sun baked it.
The Proteas openers added 82 and got through until the final over before tea when Bumrah got through the defence of Markram to be dismissed for 38.
India got another wicket immediately after the interval when spinner Kuldeep Yadav had Rickelton caught behind for 35.
Tristan Stubbs and Bavuma then buried down the hatchets and batted out the session without any further loss as the visitors went to lunch on 156-2.
The South African pair looked comfortable at the crease and took their partnership to 84 before Bavuma played a loose stroke to left-arm spinner Ravindra Jadeja to be caught mid-off for 41.
Stubbs made his way to 49 but Kuldeep got his second scalp of the innings, the Proteas number 3 poking hard at a delivery to be caught at slip and walked back to the dressing room for 49.
Wiaan Mulder then looked solid as he made his way to 13 but another soft dismissal brought his downfall as the allrounder chipped a Kuldeep delivery straight to mid-off.
At 201-5, India were sniffing an opening as they looked to level the series but Tony de Zorzi and Senuran Muthusamy, who replaced Corbin Bosch in the starting XI, added 45 for the sixth wicket.
Just as the light was fading and it looked as if the players were going off the field for bad light, India took the new ball and Siraj had De Zorzi caught behind for 28.
Kyle Verreynne came to the crease and played out four balls before the umpires deemed the light was not good enough and the players walked off to conclude the day with Senuran Muthusamy unbeaten on 25.
All-rounder Senuran Muthusamy scored his maiden Test ton (109) and Marco Jansen smashed a brisk 93 (91) to boost South Africa to 480 all out on Day Two of the second Test.
Anrich Nortje has returned to the Proteas T20I squad for the series in India next month having last represented the national team in June 2024.
Proteas front-line fast bowler Kagiso Rabada has been ruled out of the entire tour of India due to a rib bone stress injury.
Proteas captain Temba Bavuma has climbed up to number five in the world Test batting rankings after his match-winning 55 not out in the first game of the series against India in Kolkata.
