Kohli had started the third and final Test on 900 points and earned 12 points following contributions of 54 and 41.
This means he is now on 912 points and in 26th position on the all-time list, which is headed by Don Bradman (961 points).
Current number-one ranked batsman Steve Smith is second in the all-time list with 947 points.
While moving from 31st to 26th position, Kohli has leapfrogged Lara (911), Kevin Pietersen (909), Hashim Amla (907), Shivnarine Chanderpaul (901) and Michael Clarke (900).
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The India captain's next chance to gain more points will be either the one-off Test against Afghanistan in June or the five-Test series against England in August/September.
Other batsmen to improve their rankings after the Johannesburg Test include Amla in seventh (up by one place), Dean Elgar in 12th (up by two places) and Ajinkya Rahane in 18th (up by five places).
Those heading in the wrong direction are Faf du Plessis in 14th (down by two places), Lokesh Rahul in 20th (down by two places), Quinton de Kock in 27th (down by seven places) and Aiden Markram in 48th (down by 10 places).
The only bowlers inside the top 20 to improve their rankings are Morne Morkel, who has moved up two places to ninth, and Mohammed Shami, who has risen two places to a career-best 15th position.
Indias trio of Bhuvneshwar Kumar, Ishant Sharma and Jasprit Bumrah are also on the charge.
Kumar has entered the top 20 for the first time in his career after lifting two places to take 20th position, Ishant Sharma is now in 26th spot after rising three places and Bumrah is at a career-high 46th position after vaulting 36 places.
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