Team India, meanwhile, climbed to the second spot in the team rankings by virtue of their series win against England.
India have gained a spot from third to second after 2-1 win over England. In the latest list released by the ICC, Kohli leads number-two ranked Aaron Finch of Australia by 28 points, while Glenn Maxwell of Australia is third.
Kohli is ranked second in Tests and third in ODIs which makes him the only Indian batsman in top five across all formats.
India's Jasprit Bumrah, who along with England's Chris Jordan was the second most successful bowler in the series with five wickets, has narrowed the gap with South Africa's number-one ranked Imran Tahir, who claimed six wickets in the series against Sri Lanka. The two are now separated by just four points.
Samuel Badree of the West Indies sits third in the rankings. Ravichandran Ashwin is 8th in the list while Ashish Nehra is 24th.
England's Joe Root and India wrist-spinner Yuzvendra Chahal have made impressive gains after rankings released on Thursday (Feb 2) following the three-match series, which concluded on Wednesday (Feb 1).
Root finished as the leading run-scorer in the series with 126 runs for which he has been rewarded with a two-place jump putting him in fifth position.
Among Indian batsmen, next best is KL Rahul, who gained 15 places to be at 15th spot.
India's Yuzvendra Chahal, who took six for 25 in the series decider, the third-best figures in the shortest format of the game to date - has rocketed 92 places to claim 86th position.
ICC T20I Rankings (as of February 2 2017 including India Vs England series)
(Read as Rank, Player, Team, Points)
Top 5 T20I Batsmen:
1. Virat Kohli (India) 799
2. Aaron Finch (Australia) 771
3. Glenn Maxwell (Australia) 763
4. Kane Williamson (New Zealand) 758
5. Joe Root (England) 743
Top 5 T20I Bowlers:
1. Imran Tahir (South Africa) 768
2. Jasprit Bumrah (India) 764
3. Samuel Badree (West Indies) 723
4. Imad Wasim (Pakistan) 718
5. Rashid Khan (Afghanistan) 701
Top 5 T20I Teams:
(Read as Rank, Team, Points)
1. New Zealand 129
2. India 124 (+1)
3. West Indies 116
4. South Africa 115 (-4)
5. Australia 115