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.
South Africa’s ace paceman Kagiso Rabada is ruled out of the Indian Premier League with a back injury which will keep him out of cricket action for upto three months.
Star South Africa fast bowler Kagiso Rabada has appealed a ban that ruled him out of the remaining two Tests of a series against Australia, the International Cricket Council (ICC) says.
Having failed to take advantage of favourable first Test conditions, the Bangladesh batsmen have a chance to make amends against the least experienced bowling line-up South Africa have fielded in many years.
The return of Kagiso Rababa means England's faltering batsmen will face an even stronger attack than the one that ran through them at Trent Bridge.
South Africa stand-in skipper Dean Elgar says Kagiso Rabada's ban from the second match of the England series is a "big loss for Test cricket" and not just the Proteas.
South Africa fast bowler Kagiso Rabada will miss next week's second Test against England after his verbal abuse of Ben Stokes during the series opener at Lord's, the International Cricket Council (ICC) announce.
Paceman Kagiso Rabada takes 5-92 as South Africa complete an emphatic 177-run victory over Australia in the first Test at the WACA.
David Warner hits a magnificent century for Australia but could not prevent South Africa from completing a clean sweep by winning the fifth and final ODI
Fast bowler Kagiso Rabada is named South African Cricketer of the Year Tuesday in Johannesburg and receives five other awards.
Paceman Kagiso Rabada leads a brilliant South Africa bowling display to lift the Proteas to a 47-run win over Australia in the triangular one-day international series.