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Cricket South Africa said that the injury is unlikely to impact Rabada's preparation for the T20 World Cup.
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.
Delhi Capitals said Rabada had been advised to return by Cricket South Africa as a precautionary measure ahead of the ICC World Cup.
Both sides are riding high on confidence having won their respective matches on Saturday.
KKR skipper Dinesh Karthik also praised Rabada for executing the plan well, but also had a word of encouragement for his own Super Over bowler Prasidh Krishna.
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