Suresh Raina was to follow soon as he was dismissed for 1 run off 4 balls.
Mohammad Amir presented a potent threat to India's victory, dismissing the three openers cheaply.
However, Virat soon took control of the situation and put India in a stable position with Yuvraj Singh. The two piled up a partnership of 68 runs on what was a very difficult wicket to bat on.
However, Kohli unfortunately missed out on his half century by just one run when he was declared lbw to a ball by Mohammad Sami which had actually hit his bat on the way to his pad. He scored 49 runs off 51 balls.
Sami then dismissed Hardik Pandya for a duck.
Earlier, in what appeared to be a batting nightmare for Pakistan, India bowled out its arch-rivals for just 83 runs in 17.3 overs which is Pakistan's third lowest total in the T20 format.
Opting to bowl first in the third T20 of Asia Cup 2016, India had an excellent start with Ashish Nehra and Jasprit Bumrah striking early.
While Nehra dismissed Mohammad Hafeez in the first over for 4 runs off 4 balls, Sharjeel Khan (7 off 5 balls) lost his wicket to Jasprit Bumrah.
Shoaib Malik (4 off 12 balls) was sent back to the pavilion by Hardik Pandya.
The fall of wickets continued for Pakistan with Umar Akmal surrendering to Yuvraj Singh for 3 runs off 4 balls and Shahid Afridi getting run out for 2 runs off 2 balls.
Hardik Pandya brought Pakistan's innings to an end by dismissing Mohammad Sami (8 off 16 balls) and Mohammad Amir (1 off 8 balls).
For India, Pandya was the star of the innings taking 3 wickets for just 8 runs. Jadeja also put up excellent bowling figures of 2 wickets for 11 runs. Nehra, Bumrah and Yuvraj took one wicket each.
The two teams have faced each other six times in the T20 format, where India have beaten Pakistan five times, including the adrenaline-pumping 2007 World T20 Final, which India won by just 5 runs in the last over.
Winner of the 2009 World T20, Pakistan will depend on their pace battery Mohammad Amir, all-rounder skipper Shahid Afridi and all-rounder Shoaib Malik.
On the other hand, after two consecutive T20 series wins against Australia and Sri Lanka, the Men in Blue are looking confident enough to knock out any opponent.
With their in-form openers, the presence of Kohli, Yuvraj, Dhoni and Raina, and the new pinch-hitter Hardik Pandya, the Indian batting line-up looks extremely powerful.
Important to mention here that India has never lost against Pakistan in any global event, may it be Asia Cup or World T20.