A drug manufacturer or doctor will have to apply to the Therapeutic Goods Administration for permission to use the drug, with at least one doctor already having started the application process.
MPs on Thursday used a rare conscience vote to remove Health Minister Tony Abbott's power over the controversial drug and instead hand control to medical experts at the TGA.
Federal Sex Discrimination Commissioner Pru Goward said Australian women and their doctors will now have a similar range of choice of abortion methods as women in the United States, Britain and New Zealand.
Ms Goward says medical and counselling guidelines should be drafted to ensure the proper and safe use of the drug, if it is approved by the TGA's medical experts.
Mr Abbott has prepared a $60 million scheme to offer counselling to women with unwanted pregnancies, including a 24-hour advice hotline and a Medicare rebate to allow for three sessions with mental health professionals.
RU486 was specifically banned in Australia in 1996, however has been licensed for use in France since 1988, the UK since 1991 and the US since 2000.
Anti-abortion groups are concerned the move will increase the number of abortions performed each year in Australia, which is believed to stand at between 80,000 and 100,000 - but this figure does not differentiate between abortions and miscarriages.