The 119 passengers left Tel Aviv in the early hours of Wednesday, Defence Minister Richard Marles confirmed to reporters in The Hague, where he is attending a summit of the NATO military alliance.
"So I can confirm that there was an assisted departure that left Tel Aviv in the last few hours," he said.
"We were very pleased to be able to provide that flight, and they've now been relocated to a place within the region, which is obviously outside of the danger zone.
"We continue to have (military) assets in the region ready to be able to provide assistance."
Mr Marles also said the government had chartered civilian aircraft for future departures "in certain circumstances".
The evacuees were taken out in a KC-30 RAAF jet.
There are still about 3000 Australians in Iran who've registered with the government for help to leave, and more than 1000 in Israel.Â
Foreign Minister Penny Wong said assisted departure flights from Iran are still not possible.
"We've got DFAT consular staff, who are in Azerbaijan, also providing assistance for those who cross that border by land out of Iran," Mr Marles said.
The evacuation was made possible after a ceasefire between Israel and Iran brokered by the US on Tuesday (AEST).
The latest conflict erupted on June 13, when Israel fired missiles at Iran in a bid to blow up military assets, arguing it was on the cusp of developing nuclear weapons.
The battle took a turn on the weekend when the US launched a bombing raid on Iran, blowing up three underground nuclear facilities.
The airspace in both countries was shut to passenger aircraft, leading to the evacuation of Australian embassy staff and their dependents from Tehran.
But the current ceasefire has not calmed the fears of Iranians in Australia.
The Australian-Iranian community lives in fear of US or Israeli bombs killing their friends and family while also worrying about the threat posed by Iran's autocratic Islamic government to their loved ones.
No one person or voice can speak for an entire group, Australian Iranian Community Alliance vice-president Suren Edgar said, however, he believed most Iranians were not happy with the current regime.
"This is not our war, we didn't create this war but we are paying the price," he told AAP.
"If the outcome of the ceasefire would be to keep the Islamic Republic in power, that won't be safe for the international community and won't be safe for the people inside Iran."
For some, like Persian Australian Community Association member Nader Ranjbar, there was hope the conflict could help de-stabilise the Iranian autocracy and pave the way for a new, democratic government.
Without a new regime, he is concerned that the current administration will intensify its persecution of the Iranian people.
"That's my worst fear," he told AAP.
"That somehow they get away from this mess and the first thing they do is start killing Iranian people.
"We are all worried about our family and friends and the whole country."
There was also confusion about whether the ceasefire will last.
Iran's state media on Tuesday reported the truce and Israeli Prime Minister Benjamin Netanyahu confirmed he had accepted the ceasefire after achieving his war goals.
