Burger, 29, experienced discomfort in his lower back.
Rajasthan Royals' seasoned campaigner Trent Boult on Sunday picked Riyan Parag and Nandre Burger as the two players in his side who would have a key role to play in the ongoing IPL season.
Riyan Parag hammered seven fours and six sixes, and took Anrich Nortje to the cleaners in the final over, scoring 25 runs.
Heinrich Klaasen blasted Durban's Super Giants into their first-ever SA20 final as the Super Giants comfortably beat Joburg Super Kings by 69 runs in Qualifier 2 at the Wanderers
India vs South Africa: In a spectacular day for the bowlers, there were mind games being played too
Virat Kohli looked a million dollars as he did extensive simulation for South Africa's left-arm pacer Nandre Burger but Shreyas Iyer's problems seemed to continue while facing a barrage of short balls
Opener Tony de Zorzi slammed a magnificent maiden hundred to complement a superlative effort by his team's bowlers as South Africa humbled India in the second ODI
Shreyas Iyer scored a flamboyant half-century to guide India to victory over South Africa in the first ODI encounter on Sunday.