The hosts will be led by wicketkeeper Pant in a must-win match starting Saturday in Guwahati after they lost the first Test in the two-game series.
"He is doing fine, he is getting better. He was keen on playing this Test match, but his body didn't allow it," Pant said.
Batsman Gill suffered neck spasms in the first innings of the opening Test and pulled out of the remainder of the match, spending a night in hospital.
He travelled with the team to Guwahati but was forced out as the medical staff believed playing him would risk aggravating the injury.
"From a captaincy point of view, when you see his resilience, that even when your body is not supporting, but you want to push it for your team," said Pant.
"That's the kind of mindset we want to inculcate, and he did it from the front."
Top-order batter Sai Sudharsan is expected to replace Gill in the team, which will be announced at the toss.
South Africa, led by Temba Bavuma, are chasing a first series win on Indian soil since Hansie Cronje's team triumphed there in 2000.