Maharaj took three wickets from 55 overs of left-arm spin.
The pitch had already started turning as India sent in Ashwin and Jadeja to make quickfire strikes on the South African batsmen.
Rohit Sharma and Mayank Agarwal inflicted a record-breaking partnership against South Africa on Thursday as India reached 324 for one at lunch on the second day of their opening Test.
The 28-year-old Agarwal put on a record 317-run opening stand with opening partner Rohit Sharma to set the tone for India's dominance.
He smashed six sixes and 23 fours in a 371-ball knock, using the reverse sweep to good effect as he made his mark in just his fifth Test.
India then suffered two quick blows. Cheteshwar Pujara went for six and skipper Virat Kohli for 20.
Sharma fell one short of his highest score of 177 after being stumped off spinner Keshav Maharaj. He hit six sixes and 23 fours.
The opening pair tore in to the opposition bowling after the hosts resumed on 202 for no loss.
The 28-year-old Agarwal moved from his overnight 84 to complete his maiden Test hundred in his fifth match with a single off Maharaj early in the morning session.