First thing to check with air freight is what the direct flights are. Qantas and South African Airways fly widebodies directly from Sydney to Johannesburg, so that's your easiest route (no transshipment from one plane to another) - a good place to start is the cargo departments of either airline in Sydney.
Sea freight might be cheaper, but a) very slow and an unreliable arrival date (plus port fees that can even it out), and b) I am not sure Melbourne to Cape Town is a common container route, there wouldn't be a single ship calling at both ports in that direction, and that means transshipment, more time and chances of things going wrong.
As always, consider that at the price of two-way shipping, it may be cheaper and easier to just rent/buy and sell back a bike at your destination.
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