Kumar had taken six wickets across two South African innings in the first Test, which India lost by 72 runs.
In the rankings for the Test batsmen, Australia's Steve Smith remained on 947 points in first position, but there was some movement just behind him.
India skipper Kohli lost the second position to his England counterpart Joe Root and was placed third ahead of Kane Williamson, who was ranked third before.
Pujara's scores of 26 and four resulted in his total falling by 25 points.
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South Africa's Hashim Amla and Dean Elgar slipped three places apiece to finish in 10th and 16th positions respectively, but AB de Villiers jumped five places to 13th with a slot in the top-10 firmly within his sights.
South Africa opener Aiden Markram, who was the player of the tournament in the ICC U19 Cricket World Cup in 2014, and India all-rounder Hardik Pandya were the other big movers from the Newlands Test. Markram moved up six places to 48th, while Pandya was ranked 49th after rocketing 24 places.
India though, continued to be the top-ranked Test team with 124 points followed by Soutt Africa (111), Australia (104), New Zealand (100) and England (99).
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