UPDATE: On 28 March 2020, the Order mentioned in the original answer below has been replaced by the Public Health (COVID-10 Air Transportation Quarantine) Order 2020. The new Order now imposes compulsory, police-supervised quarantine in a designated quarantine facility (typically a hotel) for all overseas arrivals at the first point of entry.
What this means is that you will be taken directly from the airport to the quarantine facility immediately on arrival. Any further travel can only occur after the 14 day quarantine period is completed.
Other States have imposed similar requirements.
As noted in the guidelines (emphasis added):
All travellers must isolate for a period of 14 days after they have entered Australia. If you need to transit domestically, you may complete this transit and then begin your precautionary 14 day self-isolation period. If you have a layover, you must remain in the airport or self-isolate in your accommodation for the transit period.
This means you are allowed to transit from an international flight to a domestic flight until you arrive at your first intended Australian destination, and then self-isolate from there.
In terms of the exact regulations, it will depend on the State in which you first arrive. (It is unclear why the regulations were made by the State and territory governments instead of the federal government.) For example, if you first arrive in Sydney, then you are subject to the Public Health (COVID-19 Quarantine) Order 2020 (NSW). The requirement is set out in subclause 5(1)(a) of the Order (emphasis added):
(a) travel from the point of arrival in New South Wales to premises suitable for the person to reside in during the quarantine period,
(b) except in exceptional circumstances, reside in the premises during the quarantine period,
This means that self-isolation requirement commences in the first place you reside.
In terms of the transit exemption, this is set out in subclause 5(2)(b):
(2) The direction under subclause (1) [the self-isolation requirement] does not apply to the following persons ...
(b) a person who arrives in New South Wales at an airport and does not leave the airport before taking a flight out of New South Wales.