Kohli, who stroked 119 and 96 in the two innings in the first Test against South Africa, was the second highest-ranked Indian after Cheteshwar Pujara, another centurion in the same match in Johannesburg, who remained on seventh spot after earning 37 rating points.
South African A B de Villiers, one of the two South African centurions to help draw the Johannesburg Test, leads the rankings. He leads compatriot and second-ranked Hashim Amla by 25 ratings points.
Philander has dislodged team-mate Dale Steyn, who had been at the top of table since July 2009 when he went past Sri Lanka's Muttiah Muralitharan. Overall, Steyn spent 186 matches at the number-one position, the second-most ever after Muralitharan.
Philander had entered the Test trailing Steyn by four ratings points. While Philander recorded figures of four for 61 and three for 68, Steyn managed just one wicket. The contrasting performances resulted in Philander gaining 13 ratings points and Steyn conceding 13 ratings points.