Can I apply for citizenship if I wasn't born in here and only one parent is South African

The short answer
Yes, but you need to get a South African birth certificate first.

The whole question
I was born to a Botswana mother and a South African father (deceased). My birth was not registered in South Africa but I hold a Botswana birth certificate that has my father's name on. Do I qualify for South African citizenship?
The long answer
This is what the law says:
A child born outside South Africa and of which at least one of the parents was a South African citizen at the time of the child's birth has a claim to South African citizenship by descent. The child's birth must, however, be registered in South Africa for the child to acquire South African citizenship.
Where a child is born to one (1) or more South African citizen parent/s but such child’s birth is never registered in accordance with the Births and Deaths Registration Act, the process that such child would need to go through in order to become a South African citizen is known as the late registration of birth process.
So, you would qualify for citizenship once you had got through the hurdle of late registration
(Of course, you will not have a valid South African ID to submit as you are going through the whole LRB process to fulfil the condition of having your birth registered here in order to qualify for citizenship by descent.)
As your South African parent is deceased, Home Affairs (DHA) would probably start off by investigating your status to check that you do have a right to South African citizenship. You would need to have your father’s South African ID to prove that he was South African and a certified copy of your Botswana birth certificate.
Once you have got the LRB done, you will need to submit documents to Home Affairs to apply for South African citizenship by descent:
But unfortunately, the LRB process is a very long-drawn-out difficult business and there is a substantial backlog of people waiting for their LRB interviews

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