Elgar took a nasty blow on his helmet in the ninth over of South Africa's second innings which forced early stumps on day three but the match resumed next day after deliberations between the captains and match officials.
After receiving a lot of flak for losing the opening two Tests in Cape Town and Centurion, Kohli's men scripted a dramatic turnaround in the third and final Test against South Africa to win the match by 63 runs.
With this win, India also kept their unbeaten record intact at the Wanderers. It was their second victory in five Tests with the other three being draws.
India had already conceded the Test series after losing the opening two matches but Kohli lauded his team for showing character and guts and pull off a dramatic win in the third Test in Johannesburg.
Shami ended with career-best figures of 5/28, while Jasprit Bumrah (2/57), Ishant Sharma (2/31) and Bhuvneshwar Kumar (1/39) shared the other five wickets.
The day 3 of the third Test between South Africa and India was called-off early after a discussion by the match umpires with the respective team captains following the incident where a back of a length delivery from Bumrah hit Elgar on his helmet.
Kohli was criticised for his bold selection decisions in the ongoing Test series against South Africa with former batsman Virender Sehwag saying there is no one in the dressing room to point out Kohli's mistakes.
Asked if India would be willing to continue with the game after repairs had been made to the pitch, he replied, "It could be unfair to one of the sides."
Match officials stopped play in the third and final Test between South Africa and India on Friday in a rare move over the possibility that the pitch at the Wanderers was too dangerous for batsmen.
Chasing a stiff 241 on a tough pitch, the hosts ended the day three 17/1 in 8.3 overs. They lost opener Aiden Markram (4), caught behind off Shami's bowling.
India vs South Africa 3rd Test Match: Watch Ind vs SA third Test Cricket Match Live Streaming from Johannesburg at Sony Cricket Live TV and Get Latest Cricket Score ball by ball Commentary Live updates at India TV.
The mega player auctions of the IPL will be held on February 27 and 28 in Bengaluru, the last two days of the third and final Test between India and South Africa.
South Africa have managed to build important partnerships - du Plessis and de Villiers putting on 114 runs in the 1st innings in Cape Town, and then De Villiers and Elgar stitching 141 in the 2nd innings at Centurion Test - which made the difference.
Speaking about India's chances in the third and final Test, Sehwag made a blatant statement that the visitors cannot win the match if they bat first in Johannesburg.
Watch Live Cricket Streaming Online India vs South Africa Third (III) Test day 4 Cricket Match Ball by Ball Commentary, Ind vs SA Cricket Score Live Updates on Sony Sports through our Live Blog at India TV
Meanwhile, South Africa have already sealed the three-match series, after winning the first Test in Cape Town by 72 runs and the second Test in Centurion by 135 runs.
India had lost the first Test in Cape Town by 72 runs and were beaten in the second match at Centurion by 135 runs to surrender an unassailable lead to the hosts.
The 32-year old pacer added that the hosts will not lower their guard in the third Test against India starting in Johannesburg on Wednesday as they eye a 3-0 series whitewash.
Shastri believes Virat Kohli and Co. should have landed in South Africa little earlier to acclimatise and called for more preparatory time ahead of future overseas tours.
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