Paceman Shardul Thakur, who replaced Bhuvneshwar Kumar, accounted for three South African batsmen while Khaya Zondo top-scored for the hosts with his 54-run knock.
India are leading the series 4-1.
Brief Scores:
South Africa: 204 all out in 46.5 overs. (K Zondo 54, Aiden Markram 24; S Thakur 4/52, Jasprit Bumrah 2/24).