As long as you've been admitted to NZ for 1 year, you can choose to have your application processed in Sydney, or in Pretoria. There is a spot on the form where it asks which office you'd like to use.
Looks like the processing times are very similar, with Sydney coming in just one month faster. If you are required to do an interview, it might be better to process out of Sydney, so you wouldn't have to travel back to SA.
Good luck!