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India were bowled out for 131 in the second innings after South Africa had posted 408.
Elgar made an unbeaten 140 and Bedingham an assured 56 as South Africa reached 256 for five, a lead of 11 runs.
Kohli and Iyer were invloved in a 68-run partnership for the fourth wicket.
South Africa is the only regular Test-playing country where India have yet to win a series.
South Africa are justifiably proud of their unvanquished status against India at home and the Proteas can be expected to go all out to preserve this.
Rabada has been struggling with a heel injury and Ngidi with his ankle, but South African coach Conrad said they are still part of the squad.
The Kerala batter scored his first international century on Thursday eight years since making his India debut.
Bavuma will captain the Proteas in the two-Test series which starts on December 26.
Mumbai Indians have traded their all-rounder Cameron Green to RCB in an all cash deal.
Afghanistan wrapped up their best ever World Cup campaign with four wins and also sealed a place in the Champions Trophy.