Ravi Ashwin spun the hosts to a thrilling victory in Bangalore, but it was the actions of the Australian skipper when dismissed which became the talking point as India levelled the series at 1-1.
Chasing 188 to win, Australia looked all set at 74-3 when captain Smith was trapped in front by a Umesh Yadav shooter.
Wondering whether to review or not Smith appeared to look towards the away dressing room for help, a clear contravention of the rules of the game, forcing umpire Nigel Llong to intervene.
A visibly furious Kohli launched into Smith on the field as he set back off towards the pavilion.
And he refused to back down after the match stopping short of calling the visiting skipper a ‘cheat, but still accused Smith and the Australian team of underhand tactics.
"I saw that two times when I was batting out there," Kohli said when quizzed about the incident. "I pointed it out to the umpires and twice I have seen their players looking up there for information and that's why I was adamant.
"When he turned back that's when the umpires knew what was going on. We told the umpires they had been doing that for the last three days and that had to stop.
"There are lines you don't cross on the cricket field. I won't mention the word but it falls into that bracket. I would never do something like that on the field."
Asked if the word in question was "cheating" Kohli said: "I didn't say that, you did."
Smith admitted afterwards he regretted his actions and apologised to Kohli and the Indian team before looking to move on from the incident.
“It was a bit of a brain fade and I shouldn't have done that,” he said. “As far as I'm concerned the game was played in good spirits and nobody crossed the line."
The four-match series continues in Ranchi on March 16.