Pathan's comments came as India defeated New Zealand in the second Test by 372 runs to clinch the two-match series 1-0.
With this win, India also became the number one ranked Test team.
"As I have said earlier and saying it again @imVkohli is the best Test Captain India have ever had! He's at the top with the win percentage of 59.09 per cent and the second spot is at 45 per cent," tweeted Irfan.
Kohli on Monday became the first player to record 50 international wins in each format of the game.
The victory over New Zealand also means India sealed the two-match series 1-0, and now Kohli's side will head to South Africa for three Tests and three ODIs, beginning December 26.
"Congratulations @imVkohli. The first player with 50 international wins in each format of the game," BCCI tweeted.
Resuming Day 4 at 140/5, overnight batters Rachin Ravindra (18) and Henry Nicholls managed to add just 22 more runs to the total before the former was scalped by Jayant Yadav and the visitors were staring down the barrel, still needing 378 runs for a win with just four wickets in hand.
In his very next over, Jayant Yadav dismissed Kyle Jamieson and Tim Southee and it seemed that the hosts would wrap up the match before the lunch break on Day 4.
The final two wickets also fell in quick succession and in the end, New Zealand was bowled out for 167, handing the hosts a 372-run win. (ANI)