Gill, who retired hurt in the first innings of the Kolkata test which India lost by 30 runs, travelled with the team to Guwahati on Wednesday.
"He is definitely recovering really well. Now, the decision (whether to play him or not) will be taken tomorrow evening," Kotak told reporters.
"If we have a guarantee that very likely he won't have this issue again, then he will play. If there is a doubt, he will take rest (for) one more game, because it won't be helpful to the team."
Vice-captain Rishabh Pant will lead the hosts if Gill misses the second test which starts on Saturday in Guwahati.
"Any team would miss a player and a captain like Shubman. But if he misses out because of an injury, then we have plenty of good players who should step up and perform for the team," added Kotak.
If Gill is absent, Sai Sudharsan could reclaim his spot in the top order, with Devdutt Padikkal and Nitish Kumar Reddy also available as alternatives.
India and South Africa will meet in three one-day internationals and five T20 internationals between November 30 and December 19.