Firstly, he may not have made an application for naturalization. If he went overseas from S. A., he must have made an application, because you had to naturalize in order to get a S. A. passport.
Secondly, the National Archives of S. A. is problematic in that, unless you enter the name as it was entered by the person doing it, you won't find it. E. g. I knew that my grandfather had made an application, but it was not listed under ZETLER. Eventually I looked for him under his first first name, and that was how I found it, listed as ZELTER!