It ends years of Canberra siding with the United States by actions on the treaty to ban the deadly weapons and comes as Australia looks to nuclear submarines to boost its navy.
Signatories to the treaty agree not to develop, test, produce, acquire, possess, stockpile, use or threaten to use nuclear weapons.
But the world's major nuclear superpowers, like the US, the UK, Russia, China or India are not signatories to the ban.
Australia's abstention came on Saturday morning, Canberra time, and puts it on the fence of the contentious issue.
It follows Foreign Minister Penny Wong criticising Russia for blocking progress at a major nuclear non-proliferation conference in August.
Russia barred a consensus outcome on the final document at the tenth Review Conference of the Treaty on the Non-Proliferation of Nuclear Weapons following a four-week review of the cornerstone disarmament treaty.
At the time Senator Wong said Russia was "deliberately obstructing progress" on meaningful action on nuclear disarmament, non-proliferation and the use of atomic energy".
Australia also recently faced criticism from nuclear powers for joining a Pacific push to help deal with the consequences of nuclear testing.
New Zealand, a signatory to the nuclear weapons ban, has previously pushed for Australia to join.
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