Chopra, on a comeback trail for a place in the national squad, sent a clear notice to the selectors with a solid carrer best unbeaten knock of 239 while Badrinath also staked his claim with attacking 200.
At stumps, the visitors were struggling at 93 for 2.
Resuming at their overnight score of 354 for 4, Chopra and Badrinath sent the visitors on a leather hunt as both added 234 runs in 61.3 overs without getting separated before Mohd. Kaif applied the closure.
It was the day South African bowlers along with their skipper Boeta Dippenaar will not forget easily. Nothing went right for the visitors as they suffered the wrath of belligerent Indian batsmen without any success.
Chopra, overnight 137, and Badrinath (77) started the day cautiously but once they got into their rhythm, all hell broke loose and the South African bowlers scurried for the cover.
Badrinath hit three off de Wet to race to his century in 97.5 overs and after that he and Chopra kept the scoreboard moving at a very fast pace.
Dippenaar used six bowlers, reshuffled them time and again but none of them could breach the defence of Indian batsmen.
By the end of 123rd over, Chopra had reached to his individual score of 173 while Badrinath was on 150.
The batsmen sent the ball to all directions of the park and South African fielding wilted under this blitz.
Chopra crossed his 200 in 143 overs and Badrinath took 7.3 overs more to reach to his double century and at that stage the Indian innings was declared.
Chopra, who was dropped by Ontong off his own bowling when he was at 231, stayed at the crease for 623 minutes, faced 461 balls and hit four sixes and 19 boundaries in his knock.
Badrinath's 200 were studded with three sixes and 17 fours.
He was at the crease for 400 minutes and faced 307 balls.
The South Africans started their reply cautiously and openers M Van Wyk and W Coetsee put up 55 runs for the opening wicket.
The partnership was broken when Coetsee was caught by Kaif off Pragyan Ojha. The batsman made 18 (1x4).
The visitors suffered another blow just before the stumps when Hashim Amla was run out at his individual score of 8 and team total of 78.
At stumps, Van Wyk was batting on 53 (8x4) and Dippenaar was on 3.
India 'A' (First Innings): 588 for 4 decl (Akash Chopra not out 239, Parthiv Patel run out 110, S Badrinath not out 200)
South Africa 'A' (First Innings): 93 for 2 (M van Wyk batting 53, W Coetsee c Kaif b Ojha 18)