Nima and Dawa have been staying at the Children First Foundation retreat in Kilmore since coming to Australia.
The 15-month-old twin girls, Nima and Dawa Pelden, were joined at the stomach and had grown up facing each other, unable to move independently.
About 36 specialist split into two teams -a team for each child- participated in the procedure and Lead surgeon Dr Joe Crameri said the girls coped very well and have a good chance of full recovery.
In 2009, the same hospital performed a successful operation to separate Bangladeshi conjoined twins.
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The girls were known to share a liver, but it was not known before Friday whether they also shared part of the bowel, which would have complicated the surgery.
The girls, who were joined from the lower chest to just above the pelvis, arrived in Australia with their mother Bhumchu Zangmo about a month ago.
But on Friday afternoon he said once they were able to successfully separate their livers without compromising their health and access the bowel without impediment the surgery was less complicated.
"And really the main challenge today, as we thought, was getting the abdomen reconstructed so both areas were closed over".
Their operation was previously postponed after last-minute checks revealed the sisters were not ready, giving them more time to gain weight and grow stronger.
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During the operation, the twins' mother planned to wait at a Buddhist temple and pray.
Doctors successfully divided the twins' liver.
Dr Crameri congratulated the team and said the extraordinary amount or work and preparation put into the operation had "paid dividends".
Zangmo would spend the day praying and meditating, she added.
"We saw two young girls very ready for surgery, were able to cope very well with the surgery and now in recovery doing very well, " he said.
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The Victorian state government pledged to cover surgical costs, with other funds raised to go towards the girls' Australian rehabilitation and return home to Bhutan.