Kohli, who recorded his 21st century at Centurion, got to the rare feat in his 65th Test after vaulting from 880 points to 900 points.
Kohli struggled to make runs like his teammates during India's 72-run defeat against South Africa in the opening Test in Cape Town.
Kohli would be eyeing the chance of reaching the zenith in all three formats since he is the currently holding the numero uno spot in the ODIs and T20Is.
The Rajkot-born batsman returned to the number two position after playing a brilliant knock of 143 in the Nagpur Test which helped his side to register a huge victory by an innings and 239 runs against Sri Lanka.
The change in rankings came following defending champions Australia's 2-1 victory over England in the ICC Women's Championship series.
Proteas returned to the number one position in ICC ODI rankings following their 104-run victory over Bangladesh in the second ODI on Wednesday.
India, who reached the final of the ICC Women's World Cup in June this year, have gained three points to take their tally to 116 points.
Rohit's 296 runs in the series, which included a 125 in the last match in Nagpur, contributed significantly to India's convincing victory over the world champions.
Statistics favour the Indian cricket team in Kolkata ODI as they have not lost to Australia in the second ODI of a bilateral series at home in the last three outings.
However, no Indian bowler figure in the top-10 list. Pacer Bhuvneshwar Kumar (13th) is the lone Indian in top 15.
Shami's career has been plagued by injuries but if that part is taken care of, he can be a world-class bowler consistently, feels Kohli.
Incidentally, the match which put Jadeja on top of the heap is also the one where he breached ICC Code of Conduct to be handed a one-Test suspension.
The Indian skipper has scored 356 runs in the ongoing ICC Women's World Cup 2017, including the match-winning 109 against the Kiwis on Saturday.
Pakistan's emphatic win over India in the Champions Trophy final has helped them to move to the sixth spot in the latest ICC ODI rankings, the men in green are now closer to direct qualification for the 2019 World Cup in England.
Virat Kohli dethroned South Africa captain AB de Villiers from the top after smashing two half-centuries in three ICC Champions Trophy 2017 matches so far.
A tremendous bowling performance in the third Test against Australia has catapulted India's Ravindra Jadeja over Ravichandran Ashwin to grab the pole position in the latest rankings for ICC Test bowlers.
Virat Kohli maintained his top spot in the latest ICC rankings of T20 batsmen while India have gained a spot by virtue of their series win against England to climb to the second spot in the team rankings.
Indian captain Virat Kohli today slipped a rung to third in the ICC rankings for ODI batsmen but his predecessor Mahendra Singh Dhoni gained a spot to be 13th in the latest list issued here.
Left-arm spinner Ravindra Jadeja’s maiden 10-wicket haul against England in Chennai has propelled him to the second spot behind star off-spinner Ravichandran Ashwin in the list of ICC Player Rankings for Test Bowlers.
India's dashing batsman Virat Kohli retained his second spot in the latest ICC Player Rankings for ODI Batsmen issued today. While South Africa's AB de Villiers is still the number one ranked batsman with 13 points ahead of Kohli.
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