Wicketkeeper-batsman Quinton de Kock will be available for the ODI series after his abrupt retirement from Test cricket on Thursday, while all-rounder Dwaine Pretorius earns a recall.
India will now lock horns with South Africa for three Tests and three ODIs, beginning December 26.
South Africa captain Faf du Plessis will miss the remainder of his side's limited overs tour to Sri Lanka after injuring his shoulder in Sunday's 78-run victory that clinched the one-day international series.
But the focus will be on 19-year-old Gill, who has broken into the Indian Test squad for the three-match series against the Proteas, starting on October 2 in Visakhapatnam.
Replying to India's 497-9 declared, South Africa were all out for 162
Matt Henry produced a career-best seven for 23 in a spectacular display of pace bowling as New Zealand skittled out South Africa for 95 in two sessions to take charge of the opening Test in Christchurch on Thursday.
India captured four wickets to reduce South Africa 'A' to 179 for 9, who go into day four with a paltry lead of 40 runs in the second innings.
Virat Kohli's men ticked almost all the boxes during their 203-run win in the opening encounter in Visakhapatnam and they would like to maintain the same intensity in their bid to seal the series in Pune itself.
Vernon Philander took two wickets in as many balls to leave Pakistan on 17 for two wickets at the end of the first day of the third Test after they had rallied earlier on Friday and bowled hosts South Africa out for 262.
Captain Shreyas Iyer and semior batsman Ankit Bawne hit patient half centuries after early stutter as India 'A' won the two-match series against South Africa 'A' by 1-0 margin after the second unofficial Test ended in a draw in Bengaluru on Monday.
Rohit Sharma continued his sensational run as the Test opener with his third hundred of the series, allowing India to regain control of the proceedings after a top-order collapse on Day 1 of the third and final Test against South Africa.
Led by Quinton de Kock, South Africa's 44 cricketers, who are part of a men's high performance squad, have returned to training amid the COVID-19 pandemic after getting approval from the country's sports ministry. South Africa has reported more than 1,38,000 COVID-19 cases with over 2,400 deaths.
A desperate India seek to restore parity against South Africa and remain consequential in the World Test Championship.
Markram's good form augurs well for the Proteas
Rookie opener Sarel Erwee savoured a maiden century as South Africa dominated day one of the second Test against New Zealand in Christchurch to be 238 for three at the close on Friday.
South Africa will have to produce an exceptional batting performance to get back into the contest when skipper Faf du Plessis and Zubayr Hamza return to the crease in Ranchi on Monday.
South Africa 'A' fast bowler Lungi Ngidi, on a comeback trail after injury, bowled Gill, who made a classy 90 in the first innings to leave India 'A' at 10 for one.
South Africa trail by 439 runs and will need to bat for much of the weekend to stay in the contest and avoid going 2-1 behind in the four-Test series.
South Africa have named six uncapped players in their 17-man squad for the first two Tests of the four-match series against England as new coach Mark Boucher seeks to revive the fortunes of the ailing side. Batsmen Pieter Malan and Rassie van der Dussen, fast bowlers Dane Paterson and Beuran Hendricks, all-rounder Dwaine Pretorius and wicketkeeper Rudi Second will all hope to make their debuts in the first Test starting in Pretoria on December 26.
Images from Day 4 of the 3rd Test played between South Africa and England in Port Elizabeth on Sunday
IMAGES from Day 4 of the 2nd Test played at Newlands in Cape Town on Monday
Kagiso Rabada proved the destroyer-in-chief with 4-103, assisted by Anrich Nortje who took three wickets for 56 runs as England fell short by 107 runs.
Rohit scored 212 and Ajinkya Rahane contributed 115 as India declared their first innings at 497 for 9. South Africa are 9 for 2 at close of play.
Cricket South Africa on Monday announced the appointment of Amol Muzumdar as interim batting coach for their next month's three-match Test series against India.
Fast bowler Anrich Nortje, wicketkeeper/batsman Rudi Second and spin bowling all-rounder Senuran Muthusamy have been included in the 15-man squad that will be captained by Faf du Plessis.
South Africa bowled England out for 181 in their first innings and had built up a significant 175-run lead by the close of play on the second day of the first Test at Centurion Park on Friday. Images from Day 2 of the first Test between South Africa and England at Supersport Park in Centurion on Friday.
South Africa's fiery seamer Duanne Olivier took five wickets as the hosts powered into the ascendancy on day two of the third and final Test against an outgunned Pakistan at the Wanderers on Saturday.
'It was absolutely a risk worth taking. I wouldn't swap it for anything. To be a World Cup winner, I'd take that any day of the week. Even if I didn't play another game of Test cricket I've got that to look back on with great memories, the pinnacle of my career'
Images from the Day 2 of the second Test at Newlands on Saturday.
James Anderson marked his 150th Test and return to the England attack with the first-ball wicket of home opener Dean Elgar, and Sam Curran also grabbed four wickets before Quinton de Kock rallied the Proteas. Images from Day 1 of the opening Test played between South Africa and England at Centurion on Thursday.
The Indian team's strategy is expected to undergo paradigm shift with some players getting a subtle yet stern message to lift their games as they face an embarrassing possibility of a clean sweep against South Africa in the third ODI, in Cape Town on Sunday.
'We were definitely better as in the previous Test. We just tried to control the game little bit better. Unfortunately, we couldn't get another wicket... It would have been nice to have them four-five down'
With the national selection committee and the team management deciding to promote Rohit as an opener, keeping his spunky strokeplay in mind, the next five Tests could be a make or break for the 32-year-old stylish right-hander.
KL Rahul will have to show drastically improved leadership acumen when he leads India against a buoyant South African side in the second ODI on Thursday.
Pacer Mohammed Siraj bagged his maiden 10-wicket haul as India 'A' beat South Africa 'A' by a comprehensive innings and 30 runs after stiff resistance from the middle order on the final day of the first 'Test'.
The teams for both the matches are a mix of experience and youth.
Wicketkeeper Kona Bharat has showcased his skills with the gloves and bat in the several games he has played for India 'A' in the past year or so and is close to selection in the Test team.
Whether he is batting in the middle or fielding at the boundary line, Virat Kohli's every move will be tracked, though some of that attention will now be on skipper K L Rahul.
Not just the 40 points, India will also be eyeing a 3-0 whitewash in the Gandhi-Mandela series.
India will be desperately hoping that Rohit replicates his limited overs success in the traditional format