Vernon Philander shoots up to No.3 in both -- bowlers and all-rounders -- lists in the latest ICC player rankings.
Smith retained his top spot, while Root and Williamson exchanged places within the top five in the latest ICC Test Rankings.
Both Australia and New Zealand have 102 points but New Zealand lead their trans-Tasman neighbours on decimal points and occupy the third spot.
Philander takes six as South Africa beat Australia by 492 runs in the final Test in Johannesburg, win series by 3-1.
To chase 612, Australia reach stumps on 88/3, needing to bat out the entirety of day five to save the fourth Test in Johannesburg.
Australia all out for 221 to trail South Africa by 267 runs on first innings, SA bat again to lead by 401 at the end of third day.
Bavuma remained unbeaten on 95 as Australia face a mountain to climb just to avoid the follow on after horror day in Johannesburg.
South Africa had the better of the opening day of the fourth Test against a much-changed Australia, reaching the close on 313 for six on Friday.
The pacer was also ruled out of the fourth and final Test against South Africa, which started in Johannesburg on Friday.
Darren Lehmann is to quit as Australia head coach at the end of the current Test series against South Africa amid the ball-tampering scandal.