Pant missed the 2-0 drubbing of West Indies last month after fracturing his foot during a Test against England in September, with Dhruv Jurel stepping in to keep wicket.
Pant proved his match fitness in style last week in a game between India A and South Africa A in Bengaluru, where the 28-year-old scored 90 in the second innings to guide his team to a three-wicket victory.
Fast bowler Akash Deep also returns to the squad after missing the West Indies series.
Several players, including skipper Shubman Gill and pace spearhead Jasprit Bumrah, will join the team after the ongoing Twenty20 series in Australia.
The first Test of the series against South Africa begins on November 14 in Kolkata before they move to Guwahati for the second match from November 22.
South Africa have skipper Temba Bavuma back in the squad after a calf injury kept him out of the series in Pakistan last month.
India are third in the World Test Championship while reigning champions South Africa are fourth.
INDIA SQUAD FOR SOUTH AFRICA SERIES
Shubman Gill (captain), Rishabh Pant (wicketkeeper, vice-captain), Yashasvi Jaiswal, KL Rahul, Sai Sudharsan, Devdutt Padikkal, Dhruv Jurel, Ravindra Jadeja, Washington Sundar, Jasprit Bumrah, Axar Patel, Nitish Kumar Reddy, Mohammed Siraj, Kuldeep Yadav, Akash Deep.
