Here is a very good post by Prof Grant on the matter
http://criminallawza.net/2014/05/04/one-may-intentionally-kill-another-human-being/
OP's mistake only protects him as to the point that there was not really an intruder (and therefore no threat).
Furthermore
It is worth remembering – because this issue continues to be misunderstood: one may intentionally kill another human being – so long as you are justified (such as in self/private defence) and you know/believe you are justified.
If you are not justified (such as you are not under attack), you are only liable to a murder conviction if you know/believe you were not justified – if you know that you were not under attack. If you know you were not justified, you have intention in South African law. Intention is an entirely subjective enquiry. It turns on what the accused was actually thinking.
http://criminallawza.net/2014/05/04/one-may-intentionally-kill-another-human-being/
OP's mistake only protects him as to the point that there was not really an intruder (and therefore no threat).
Furthermore
The conduct of an accused who uses a firearm will be compared to that of a reasonable firearm owner.