The 33-year-old took nine wickets in three matches against the Kiwis, including career-best figures of 6-56 in the second ODI in Christchurch.
Khaka also took her overall tally to 151 wickets in her 121 ODI appearances at the international level.
The world bowling rankings is headed by Australia spinner Alana King, going ahead of England slow-bowler Sophie Ecclestone.
The Proteas are currently in third place in the ICC Women's Championship after going down to a 2-1 series defeat in New Zealand.
Australia completed an unbeaten tour of the West Indies with a nine-wicket victory in the final ODI in St. Kitts to occupy second place with a 100 per cent record from their three matches.
Only the top seven ranked teams plus the hosts, qualify automatically, for the ICC Women's World Cup in 2029.
New Zealand clinched a 2-1 series victory over South Africa with a 66-run win in the final women's ODI in Wellington on Saturday, bringing the tour to a disappointing close for the visitors.
Amelia Kerr put on a show as she guided New Zealand Women to a record run chase of 346 for a narrow two-wicket win in the second ODI in Wellington on Wednesday.
Ottneil Baartman, Corbin Bosch, Matthew Breetzke and Dewald Brevis have earned maiden national contracts after Cricket South Africa announced the list ahead of the 2026-2027 season.
New Zealand Women were simply brilliant as they cruised to a comprehensive 92-run victory over the Proteas Women in the final T20I in Christchurch on Wednesday.
