This would have been a useful detail to include in your original post. You definitely made it sound like you were in the US and he was coming from SA to work and be paid, and had done that before.
So now it looks more like it is related to lack of ties to SA and having an American partner. Consular officers are required to look at all B visa applications under the lens of immigrant intent. Having a US partner and being from an African country makes a B visa approval very unlikely, even without the miscommunication.
If he can strengthen the ties to home, he can apply again. Honestly to apply immediately after a denial is a waste of money, but of course they'll take your money.