Rabada grabbed five wickets in each innings for an enviable match haul of 10 for 63 that helped his side to an innings and 254 runs victory.
He made a notable improvement in the latest rankings, which also take into account the second Test between Pakistan and Sri Lanka in Dubai, which Sri Lanka won by 68 runs on Tuesday to clinch the series 2-0.
Rabada has overtaken spinners Rangana Herath of Sri Lanka and Ravichandran Ashwin of India and is now on 876 points, only eight points behind second-placed India spinner Ravindra Jadeja and 20 behind top-ranked James Anderson of England.
Captain Faf du Plessis and Aiden Markram, century-makers at Bloemfontein, are among the batsmen to gain. Du Plessis's 135 not out has seen him move up two places to 14th position while Markram has gained 43 slots to reach a career-best 61st position after his knock of 143.
India batsman Cheteshwar Pujara remains in fourth spot and captain Virat Kohli in sixth position. Though India have not played a Test recently, Lokesh Rahul and Ajinkya Rahane gained a place each to be eighth and ninth in the rankings.
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