Kohli was dismissed by Junaid in all the three one-dayers.
"Before the one-day series I remember Kohli and I came cross each other and he told me that I will be playing my shots and I will score runs off you," Junaid said prior to the team's departure for South Africa.
"Given his reputation I was a bit apprehensive but once I started bowling in the first ODI and everything was working right for me I knew he would find it difficult to pick my length and I bowled him for a duck," he told 'Geo News'.
"Our bantering continued in the next two matches and it was always a big boost to pick him up cheaply because he is a class batsman," Junaid said.
Junaid, who took eight wickets in the series, said he enjoyed it when people talked about how Kohli had become his bunny.
"I knew that a series against India can either make you zero or a hero and I wanted to leave an impact. Before going to India I had realised that without getting the ball to come in I would struggle against top batsmen.
"I worked hard on my length and moving the ball both ways with my coaches and tips from Wasim Akram proved valuable to me and the series turned out to be a success," Junaid said.
The youngster said he had enjoyed the experience of playing in front of huge crowds in India.
"But I would love to play Tests against them and I think we should be playing more often against each other in a proper series... it will help both teams."
The pacer, who has already picked up three five-wicket hauls in eight Tests, said unlike other young players he was not inclined towards playing T20 cricket.
"I have got offers from some leagues but I prefer to play more county and first-class cricket now because that is the only way I am going to develop as a bowler."