The job of airlines when checking your documents when they are checking you into a flight is to make sure that you have the right to be in the country where they are taking you (and you are who you say you are, no credit card fraud has occured and you aren't a crook). As you mention, according to the rules of most countries this typically means you need a certain length of validity on your passport, long enough to 'contain' the visa that will be required for visiting.
Basically you've got to look at your passports as three separate things. They're proof to the airline that you're a allowed to board a plane, they're to show country A immigration authorities that you are leaving country A, and they're proof to the immigration authorities of country B that you can enter country V.
As I understand it right here- you'll be entering South Africa with a soon to expire South African passport..... which should be absolutely zero issue. You're South African. You don't even need a passport to live in your country.
But then you're trying to leave on a soon to expire South African passport...which the airline may find trouble with as they're working under the assumption that you're a normal South African with a soon to expire passport and the Australian immigration authorities won't let you in. Your passport is valid for showing who you are, it's this proof that you're allowed in Australia that is their concern.
But... you don't need an Australian visa. You already have a 'visa' in the form of your Australian passport. Australian immigration won't be an issue at all for you getting into the country and the airline won't recieve a fine.
I'd suggest calling the airline in advance to tell them about your situation. I'm 99% sure it will be OK, though it will make things smoother for you if they know in advance and one of their more knowledgable people puts a note on your file; if you get unlucky with someone hopeless working in the airport on the day then they might cause fuss over any number of valid but unorthodox situations.
Edit- easy version.
I'd say to rely mostly on your Australian passport. Australians don't need a visa for SA anyway. You only need to bring out your SA passport at the immigration desk in SA.