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.