Thakur (4/52), playing in place of rested Bhuvneshwar Kumar, picked his best figures in ODI cricket in this third match.
Spinners Kuldeep Yadav (1/51) and Yuzvendra Chahal (2/38) finished with 33 wickets together in this six-match series.
Aiden Markram (24) and Hashim Amla (10) made another sedate start. Thakur was impressive in his first spell, even though Markram took him for two boundaries to start off proceedings.
The pacer struck for a second time within the first power-play as a clever change of pace foxed Markram completely and he simply chipped a catch to Shreyas Iyer at cover, who caught well for a change.
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It brought AB de Villiers (30) and Khaya Zondo (54 runs) to the crease, and they rebuilt the innings with a 62-run partnership for the third wicket. They rotated the strike well and looked to be positive even against the spinners.
De Villiers and Zondo brought up their 50-partnership off 52 balls as the Proteas crossed 100 in the 19th over.
This is when things turned downwards again. Chahal bowled de Villiers in the 21st over as the batsman backed away and looked to make room. The breakthrough almost squeezed the scoring rate as the batsmen started eating up deliveries.
57 balls passed without a boundary and the scoring rate fell from 4.7/over to 4.27/over after de Villiers dismissal. In this passage of play, Zondo and Heinrich Klaasen (22) added only 30 runs off 58 balls.
South Africa had lost two wickets in the space of six balls and were reduced to 136 for five in the 32nd over. Chris Morris (4) further exasperated his dressing room as he holed out off Yadav in the deep two overs later.
Zondo and Andile Phehlukwayo (34) tried to bring some stability to the innings. In doing so, Zondo scored his maiden ODI half-century off 67 balls. He was out shortly afterwards, caught in the deep in a bid to slog Chahal.
Running out of partners, Phehlukwayo attacked the Indian bowling and managed to push the score past 200 in the 47th over, before he was last man out, returning a catch to Thakur.