The procedure, which required 20 doctors and nurses, divided their shared liver and reconstructed their abdomens.
Nima and Dawa Peldon, of Bhutan, were born joined at the torso and shared a liver, but as they grew it became hard for them to sit at the same time and stand.
"But if the connections are greater, I suspect we will need the full day, and maybe even moving into the evening", Joe Crameri, the Royal Children Hospital's head of paediatric surgery, said on Friday morning.
The operation will involve 18 medical staff, with each girl designated a separate team to care for her in theatre, plus nursing and anaesthetic support teams.
Surgeons were also able to divide the liver without compromising the girls, and are hopeful they will not have to spend time in ICU.
"We saw two young girls who were very ready for their surgery, who were able to cope very well with the surgery and are now in our recovery doing very well".
He added that the girls' mother, Bhumchu Zangmo, was "smiling, very happy, and grateful".
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.
"There will be challenges over the next 24 to 48 hours as with any surgery", Dr Crameri said.
"Mum is very relieved", Crameri said, flanked by his surgical team still dressed in their scrubs.
Born via a caesarean section past year, the girls are believed to be Bhutan's first conjoined twins.
Their mother Bhumchu Zangmo was understandably nervous before the operation, but spent today praying and meditating at a Buddhist temple.
On Thursday afternoon, the twins travelled to Melbourne from Kilmore, where they had been staying at the country retreat of the Children First Foundation.
The state of Victoria has offered to cover the A$350,000 (US $255,000) cost of the operation.
"We always felt confident that we could achieve this", lead surgeon Joe Crameri said at a news conference.