Rabada called on all the players in the tournament to seize the moment.
It was Rabada's 14th five-wicket haul in his 61st Test and his fourth in eight Tests at Centurion, but his first against India.
India were 208 for eight when bad light followed by rain brought an early close.
Kohli and Iyer went on to add 68 for the fourth wicket before both were dismissed in an inspired three-wicket spell by Rabada immediately after lunch.
The World Cup moves to Mumbai with two of the heavyweights feeling the pressure and needing to bounce back from shock defeats faced in the previous round of the mega event.
The fiery Rabada took six wickets for 50 runs as South Africa bowled out the tourists for 159 after the West Indies had been set a target of 247 to win
Fast bowlers Sisanda Magala, Anrich Nortje and Kagiso Rabada earned South Africa a dramatic 27-run win in the first one-day international against England at the Mangaung Oval in Bloemfontein on Friday.
South Africa skittled England out for 149 on Friday to win the first Test by an innings and 12 runs inside three days at Lord's and go 1-0 up in the three-match series.
South Africa could be without fast bowler Kagiso Rabada for their final warm-up match ahead of next week's first Test against England at Lord's.
Distinctly charismatic and undeniably courageous, Soumya Sarkar is making headlines and heads turn with his unforgettable knocks, only in 16 matches of his ODI career.
Two one-sided matches, with the teams batting first folding for identical scores and losing by big margins, have given the third ODI at the Zahur Ahmed Chowdhury Stadium the status of a final.
Bangladesh's troubles seem more tactical in nature, although captain Mashrafe Mortaza has said that their strategy of using eight batsmen was a confidence issue.
With debutant Kagiso Rabada’s hat-trick at Mirpur today, only two bowlers have managed to bag a hat-trick against the Tigers in ODI history.