India captain Kohli and two teammates had previously been heard complaining on the stump mic after South Africa skipper Dean Elgar survived a review.
The latest expose saw Kohli sledge home batsman Rassie van der Dussen after he survived a close caught behind appeal.
READ MORE: Langer urged to walk away after Ashes series
Kohli discussed the decision with the umpire before going to work on van der Dussen as the stump mic captured the exchange.
“Really? So you go after someone who is five years younger than you? Yeah? And then you are asking me if you sledge Rishabh (Pant)?” Kohli was recorded saying.
That remark was sparked by a confrontation between van der Dussen and India wicketkeeper Rishabh Pant in the second Test.
Van der Dussen was caught behind by Pant but replays cast doubt as to whether the ball had carried.
In India’s first innings, van der Dussen then sledged Pant, prompting the 24-year-old to tell van der Dussen to “keep your mouth shut.”
The loss denied India its first Test series win in South Africa and was an unexpected result considering the strength of their team, and the relative inexperience of the hosts.
“That people expect us to beat South Africa in South Africa is testimony to how far we’ve come,” Kohli said.
“We haven’t done it, that’s the reality. Accept it and come back as better cricketers. You’ve got to credit the opposition where it’s due.”
India was a convincing winner of the first Test in Centurion by 113 runs and that seemed to be a forecast for the series ahead.
But the Proteas levelled in Johannesburg with a gutsy fourth innings run chase and did the same again when it chased down 212 in the decider in Cape Town.
South Africa got home comfortably and finished 3-212 soon after lunch on day four.
Temba Bavuma won it with a four through square leg and then pumped his fists and let out a roar.
He was 32 not out to see his team home alongside van der Dussen on 41 not out.
The South African players in the dressing room celebrated exuberantly after their biggest win under the leadership of captain Elgar, who was appointed last year, and coach Mark Boucher.
“I threw down the challenge after the first game and the guys responded brilliantly,” Elgar said, adding he’d had some “tough chats” with his players following the big loss in the first Test.
“If you want to operate at a high performance level, have to have tough chats. If guys don’t like it, it’s up to them to deal with. I’ve got old school mentality.”
India has now had eight attempts to win a Test series in South Africa dating back to when the Proteas were readmitted into international cricket in 1992.
South Africa has won seven of the contests in South Africa, with one drawn series.
South Africa’s success in chasing down a tricky target on a wearing Newlands pitch was largely down to No.3 Keegan Petersen, who made 82 in the second innings to anchor South Africa’s series clinching innings.
He also contributed 72 in the first innings in his fifth Test and first home series.
The series was low scoring and tight throughout, partly down to the fast bowler friendly nature of the South African pitches and also the strength of both teams’ bowling attacks.
Ultimately, South Africa’s perceived weakness — its batting — prevailed against the strong Indian bowling attack led by Jasprit Bumrah, who was a threat throughout but ended with just 1-54 when it counted in the final innings of the series.
South Africa started day four on 2-101 and with the match in the balance.
But Petersen shared a partnership of 54 with van der Dussen following a stand of 78 with Elgar the day before.
When Petersen fell by cutting a ball onto his stumps to leave South Africa 3-155, India had a glimpse of victory but van der Dussen and Bavuma shut the tourists out.
For a daily dose of the best of the breaking news and exclusive content from Wide World of Sports, subscribe to our newsletter by clicking here!