The three-match T20I series is slated to get underway on December 10.
Ngidi has been sidelined due to a left lateral ankle sprain. The right-arm quick is racing against time to regain fitness for the first Test versus India.
Beuran Hendricks, who last featured in the T20 format for South Africa against Ireland in July 2021, will step in as a replacement.
Hendricks will compete for the specialist seamer role in the side with Ottniel Baartman, Nandre Burger, Gerald Coetzee and Lizaad Williams.
The Proteas have rested ace pacer Kagiso Rabada for the white-ball leg of the series against India.
South Africa are due to host India in three T20Is, three ODIs and two Tests. While the T20I series will conclude on December 14, the ODI series will be held between December 17 and December 21.
The Test series is slated to get underway on December 26 in Centurion whereas Cape Town will host the second Test from January 3.
(With Reuters Inputs)