Can I select my country as South Africa, but have USD as the base currency?

Yes, you can.

In order to create an Organization with South Africa as Country and Base Currency as USD,

• Create an organization with some other country name, say Singapore and choose the currency as USD.
• Once the organization has been created, click on the Gear icon, select Organization Profile and edit the country name as South Africa and finally click Save.

Note: This case can be applicable for all the organizations having their country as USA, UK, Canada, South Africa and India wherein the user wishes to choose a country but have a different base currency.