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.
Dr. Joe Crameri, head of paediatric surgery at Melbourne Royal Children's Hospital, said in a press conference Friday that the successful surgery was a "relief" and a "joy."
"There is nothing better in any operation than to be able to go to the parents and say 'we've been able to look after your child,'" he said. "I feel confident that they will be able to recover from this and go forward."
The twins were flown from their home in Bhutan to Australia on October 2 for the operation.
The delicate procedure took place over six hours and involved about 25 surgeons, nurses and anesthetists, according to CNN affiliate 9 News.
Crameri said that there were no surprises, despite concerns the girls' bowel may have been conjoined.
"We were very fortunate in that there wasn't any significant bowel attachment and while it was all swimming next to one another it wasn't actually connected in any major way," Dr Crameri told reporters.
He said that the girls' mother was "very grateful for everything" the doctors were able to do.
'They're getting cranky'
Funds for the girls' operation, which estimated to cost around $180,000 (250,000 AUD), according to 9 News, was raised by Children First Foundation, a Melbourne-based non profit.
"Mom said the girls are getting a little bit frustrated with each other as you would at 14 months," the charity's CEO Elizabeth Lodge said last month.
"Like any siblings they're getting cranky so mom's really looking forward to the operation happening sooner rather than later."
Born via a caesarean section last year, the girls are believed to be Bhutan's first conjoined twins.
As well as the issues with mobility and comfort, Lodge said the twins had recently been losing weight, which had been a concern to doctors who are now observing them closely.
Several members of the surgical team had previously worked on the successful operation to separate conjoined Bangladeshi twins Trishna and Krishna in 2009.
They were separated after a marathon 27-hour surgery, despite doctors initially giving them only a 25% chance of making it.
Difficult surgery
Conjoined twins occur once every 200,000 live births, according to the University of Maryland Medical Center. About 70% are female, and they are always identical twins.
Scientists believe that conjoined twins develop from a single fertilized egg that fails to separate completely as it divides.
"Although two fetuses will develop from this embryo, they will remain physically connected -- most often at the chest, abdomen or pelvis. Conjoined twins may also share one or more internal organs," according to the Mayo Clinic.
"The success of surgery depends on where the twins are joined and how many and which organs are shared, as well as the experience and skill of the surgical team."
They were previously commonly referred to as "Siamese twins," a name which originated with Eng and Chang Bunker, a set of conjoined twins who were born in Siam (now Thailand) in 1811. They lived to age 63 and appeared in traveling exhibitions. Chang and Eng both married and fathered a total of 21 children between them.
While separation surgeries of twins joined at the abdomen and other parts of their bodies, twins joined at the head are at a far greater risk.
The case of two US boys joined at the top of their skulls attracted global attention in 2016 as doctors successfully operated to separate them.
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