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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.
India managed just seven runs off the penultimate over and Sanju did not get to face a single ball.
South Africa crushed the hosts' hopes of a breakthrough series win over the Proteas.
Rabada scalped six wickets, three in each innings, to play a pivotal role in South Africa's series-levelling seven-wicket win in the second Test.
Pacer Sisanda Magala and wicketkeeper-batter Ryan Rickelton were the new faces in South Africa's 21-member squad for the three-Test series.
South Africa's director of cricket, Graeme Smith, had previously said the workload of captaining the Test side would be too much for white-ball skipper de Kock, but the selectors have had a change of heart.
The 26-year-old pacer clocked a breathtaking 156.2 kmph while bowling to Jos Buttler in the third over of Rajasthan Royals' run chase against Delhi Capitals. He bettered compatriot Dale Steyn's (154.4 kmph) record in the process.
Rabada and Kohli had a verbal exchange during one of the IPL matches between Delhi Capitals and Royal Challengers Bangalore.
The right-arm paceman returned figures of 7-0-40-1 in their 87-run victory against 1996 champions Sri Lanka in their opening warm-up match on Friday.
Onmanorama takes a look at five speed merchants who are expected to hog the limelight during the course of the tournament.