Kohli had entered the tournament 22 points behind number-one ranked AB de Villiers of South Africa, who had been No.1 since 25 February this year, and 19 points behind Australia's David Warner.
But with brilliant knocks of 81 not out against Pakistan and 76 not out against South Africa, Kohli leapfrogged de Villiers and Warner into the number one spot.
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Indian opener Shikhar Dhawan has continued his love- affair with the Champions Trophy by returning into the top 10.
The left-hander has vaulted five places to 10th following scores of 68 against Pakistan, 125 against Sri Lanka and 78 against South Africa.
Dhawan's rise means his team-mates Rohit Sharma and former captain Mahendra Singh Dhoni have slipped one place each to 13th and 14th, respectively, while Yuvraj Singh has gained six places to be at 88th spot.
Fast bowler Bhuvneshwar Kumar has led the charge of India's bowlers by vaulting 13 places to share 23rd spot with Afghanistan's Hamza Hotak.
Umesh Yadav has gained two places to be at 41st position, while Jasprit Bumrah is at 43rd after climbing up three spots.
However, Indian spinners have slipped in the latest rankings with Ravichandran Ashwin dropping two places to 20th and Ravindra Jadeja falling three places to 29th.
Australia's pace ace Josh Hazlewood has achieved the number-one position in the bowlers' rankings for the first time in his career.
Amongst the England batsmen, Joe Root has moved up one place to fourth and Ben Stokes has rocketed nine places to a career-high 20th place, while in bowlers' list, Liam Plunkett has jumped seven places to a career-best ninth spot, Adil Rashid has shot up nine places to 11th spot.
There has been no change in the top five of the all- rounders' list, which is headed by Bangladesh's Shakib Al Hasan.
Stokes has gained one spot and is now sixth, while Jadeja has broken into the top 10 in eighth position after rising three places.
In the upcoming semifinal matches of the Champions Trophy, India will have a chance to top the table.
But for that to happen, they will not only want to face England in the final but also need to retain the title.
In that case, Kohli's men will join South Africa on 119 points but will be ranked ahead of them by a fraction of a point.
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