India, who at present are busy playing Test against New Zealand, were positioned third with 110 points behind Australia (124) and New Zealand (113).
With 813 points in his kitty, Kohli was only behind South African talisman AB de Villiers and a place ahead of another experienced Protea Hashim Amla in the batting list.
Besides Kohli, Rohit Sharma (7th) and Shikhar Dhawan (8th) were the other Indians in the batting list dominated by the South Africans and the Asian giants.
No Indian bowler featured in the ODI chart, and there was no one from the country in the allrounder list as well.
As far as future team movement is concerned, fourth-ranked South Africa have a chance to climb up to second position in the ICC ODI rankings when they host number-one ranked world champions Australia in a five-match series from September 30 to October 12.
While Australia and South Africa will aim to consolidate their current positions, Bangladesh, the West Indies and Pakistan will target to improve their rankings.
World champion Australia is currently on 124 points and without an immediate threat to its top ranking with New Zealand second on 113 points. But a series win for South Africa, who are a fraction of a point behind India, against Australia could help them move ahead of the reigning ICC Champions Trophy winner.
A 3-2 series win will put South Africa in third position on 112 points, while a 4-1 series win will lift it to second position on 114 points.
For Australia, a 3-2 series win will maintain their current 124 points with a maximum drop to 118 points in the case of a 5-0 series whitewash.
Even if they also loses their preceding one-off match to Ireland and get blanked by South Africa, Australia will retain number-one position at 116 points with South Africa behind it on decimal points.
ICC ODI Team Rankings (as of 23 September 2016)
1. Australia 124
2. New Zealand 113
3. India 110
4. South Africa 110
5. England 107
6. Sri Lanka 101
7. Bangladesh 98
8. West Indies 94
9. Pakistan 86
10. Afghanistan 49
Batsmen (top 10) (as of 23 September 2016)
1. AB de Villiers (SA) 887
2. Virat Kohli (Ind) 813
3. Hashim Amla (SA) 778
4. Joe Root (Eng) 758
5. Kane Williamson (NZ) 752
6. Martin Guptill (NZ) 751
7. Rohit Sharma (Ind) 750
8. Shikhar Dhawan (Ind) 737
9. Quniton de Kock (SA) 735
10. Faf du Plessis (SA) 716 & Tilakratne Dilshan (SL) 716