The physio rushed to the pitch and Elgar was seen placing an ice-pack on his forehand.
Umpires Ian Gould and Aleem Dar began discussion and soon match referee Andy Pycroft joined them on the ground. They initiated deliberations with both the captains, players were called off the ground and play never resumed after that.
Former players Sunil Gavaskar and Jonty Rhodes, watching the proceedings from the commentary box felt that the pitch had nothing to do with the Shami delivery that hit Elgar.
The fate of the match is still unknown but courageous batting by the Indians has put them in a strong position.
Chasing a stiff 241, the hosts ended the day three 17 for one in 8.3 overs. They lost other opener Aiden Markram (4), caught behind off Shami.
Ajinkya Rahane, whose exclusion from the first two Tests led to severe criticism of team's selection policy, showed what Indian team missed out earlier in the series with his dogged 48-run knock.
The diminutive batsman was not perturbed after being consistently hit on his arms and dismissal of skipper Virat Kohli (41) as he raised a match-defining 55-run stand with Bhuvneshwar Kumar (33).
Before Rahane, opener Murali Vijay (25) and Kohli were also hit on their hands.
The on-field umpires were seen discussing the pitch condition, being consistently criticised by the commentators, but never halted play.
Rahane and Bhuneshwar's seventh wicket partnership coupled with some lusty blows from Mohammed Shami (27) in a splendid rearguard action meant that India managed to put on board 247, setting the visitors a stiff 241-run target.
The Indian skipper too showed intent to continue batting, aware that they had almost touched a defendable score.
Kohli looked class apart and went past MS Dhoni (3454 runs in 60 Tests) in the list of most runs as Test skipper.
He was bowled off an unplayable delivery that seamed in off the pitch from Kagiso Rabada (3/69) in the 50th over.
Rahane, meanwhile, played some attacking shots, primarily off Morne Morkel as Indias lead crossed 150. Kumar looked solid at the other end and the two looked to rotate strike as often as they could.
They were helped by South Africas poor effort in the field. Elgar first dropped Kumar (on 15) at gully off Morkel in the 59th over. Six balls later, Andile Phehlukwayo dropped Rahane (on 38) at deep point off Rabada.
Just before tea, the duo brought up their 50-partnership off 68 balls, almost knocking the wind out of the Proteas.
In the morning session, Rabada had hit Kohli in the 31st over and then Vijay in the 35th over, both on their hands as they failed to fend off sharp, rising deliveries.
This was after Vijay and Kohli put on 43 runs for the 4th wicket as India reached 100 for 4 at lunch.
Starting from overnight score of 49/1, South Africa quickly struck twice after India crossed 50 first thing in the morning session.
In the second over of the day, KL Rahul (16) edged behind off Philander and was caught at second slip.
Three overs later, India were reduced to 57/3 as Cheteshwar Pujara (1) was caught at second slip too, this time off Morkel. The ball just reared up off length and took the bats shoulder and Pujara could do nothing about it.
This brought Kohli and Vijay together, and the duo batted out 18.5 overs. Initially, they went through a tough passage with a lot of plays and misses.
Kohli (on 4) got a life, when Markram could not latch on to a tough half-chance at short leg off Morkel. The ball was hit straight to his hands but the reaction time was too short to make it a proper chance.
The Indian skipper then settled down and opened up to play a few more attacking shots. Vijay was down for the grind too and, for the first time in the series, held up one end for India in really tough conditions.
India crossed 100 in the 40th over. Five balls later, Rabada got the breakthrough the Proteas were looking for.
After fending length balls on a tough pitch, on the penultimate ball of the session, Vijay was bowled off a yorker that took an inside edge, ricocheted off his backfoot and onto the stumps.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)