Kohli scored 191 runs, including 127 in the final match, in India's 2-1 series win as he pushed South Africa's Hashim Amla to number three in the list, topped by Amla's compatriot AB de Villiers.
Indian skipper MS Dhoni was the next best India at number six (unchanged) while Shikhar Dhawan lost a place to be eighth. Left-handed Suresh Raina gained three places to move to 15th.
Paceman Mohammed Shami, who ended the series as the most successful bowler with 10 for 174, vaulted five places to 16th and has broken into the top 20 for the first time in his career. Off-Spinner was placed at number 18, a loss of two spots.
In the team rankings, India remain at number two with 113 points, same as South Africa, who though have a chance to snatch top spot from Australia (114) when they face New Zealand in the three-match ODI series, starting Wednesday.
If South Africa manages to win all the three matches against New Zealand, then it will reclaim the number-one position for the first time in five years after handing over the baton to Australia following its first-round elimination from ICC Champions Trophy 2009.
On the other side, if New Zealand wins the series, then it will leapfrog Pakistan into sixth position. Currently, both Pakistan and New Zealand are on equal points on 98 ratings points but the Black Caps are in seventh position when the ratings are calculated beyond the decimal point.