The bill will now be debated and voted upon in the lower house, the House of Representatives.
It was an emotional vote, which followed more than six hours of debate Wednesday night in the Senate and another four hours Thursday, in which more than half of the members spoke.
In the end, 45 senators voted to support of the private members' bill handing power over the drug to the Therapeutic Goods Administration (TGA) and 28 voted against.
Outspoken Nationals member, Barnaby Joyce said the dispute over the availability of RU486 was really one about the sanctity of human life.
"Mankind comes unstuck when it fails to respect human life,"
Senator Joyce said.
Overwhelming support
But supporters of the changes, who argue health professionals should be making decisions about who can access the drug, not politicians, hailed the result as a victory for women and good sense.
"I think that the women of Australia will be proud and confident to know that the Senate supports them, ensuring that their safety and their health is determined by the medical experts rather than by politicians," Australian Greens senator Kerry Nettle said.
Two senior government ministers Helen Coonan and Amanda Vanstone, along with former health minister Kay Patterson and former defence minister Robert Hill, supported the bill.
All Australian Democrats and Greens members of the upper house voted in its favour, as did most Labor senators.
Under current Australian laws, RU486 is available only through federal drug regulator, the Therapeutic Goods Administration (TGA), with written permission from the federal health minister.
Australian women already have access to surgical abortion with an estimated 85,000 performed annually.
Australia alone
The debate over who should control the availability of the abortion pill has divided Australia, with protests outside of parliament house.
Australia appears largely alone in the developed world with its wrangling over whether women should have access to RU486, a synthetic steroid also known as mifepristone, which allows them to abort at home.
Obstetrician Caroline de Costa, the woman who triggered the latest RU486 controversy in an article in the Medical Journal of
Australia (MJA) last October, said the drug had been used in about two million abortions worldwide.
The World Health Organisation has also added RU486 to its list of essential medicines for developing countries.
RU486 was specifically prohibited in Australia under a 1996 act of federal parliament, yet it has been licensed for use in France since 1988, in the United Kingdom since 1991 and in the United States since 2000.
When used in combination with another drug, such as misoprostol, RU486 results in complete abortion in between 93 and 98 per cent of cases.
In the remainder, the abortion needs to be completed by an appropriate qualified doctor.