The departure ends days of uncertainty after five of the seven squad members who sparked a diplomatic furore by seeking asylum in Australia reversed their decisions and rejoined the team in Kuala Lumpur.
Members of the squad declined to speak to reporters as they spent several hours at the airport checking in and waiting for their flight on Monday night.
Meanwhile, the two players who remained in Australia joined a training session with the women's A-League club, the Brisbane Roar.
The club released photos of Monday's training session, with Fatemeh Pasandideh and Atefeh Ramezanisadeh smiling and wearing the Queensland team's colours.
Brisbane Roar CEO, Kaz Patafta said his club welcomed and supported the players but declined to comment further, directing questions to the Department of Home Affairs.
"We remain committed to providing a supportive environment for them whilst they navigate the next stages," he said.
Asian Football Confederation general secretary Windsor John earlier told The Associated Press his organisation was supporting the Iranian team in Kuala Lumpur.
He said the AFC was told they are flying to Oman, but that isn't their final destination and that he wasn't aware of their full travel plans.
Asked if the confederation was satisfied that the women would be safe back in Iran, Mr Windsor said the AFC and FIFA would check up on them regularly with the Iranian football federation "as they are our girls as well".
The squad flew from Sydney to Kuala Lumpur a week ago after being knocked out of the Women's Asian Cup in Australia, initially leaving behind six players and a support worker who had accepted protection visas.
Four players and the staffer have since rejoined the team in Kuala Lumpur, the latest flying in on Monday.
No reasons have been given for the changes of heart. The Iranian diaspora in Australia blames pressure from Tehran.
Mr Windsor said at a news conference earlier his confederation had not received any direct complaints from players about returning home, despite media reports their families in Iran could face retaliation for the team failing to sing their national anthem before the opening match.
The silence during the anthem was variously reported as an act of resistance or a show of mourning. The team didn't clarify, and it sang at the opening of a later match.
"We couldn't verify anything. We asked them and they said, 'No, it's okay,'" he said.
"They are actually in high spirits ... they didn't look afraid."
Iranian authorities welcomed the women's decisions to reject asylum as a victory against Australia and US President Donald Trump.
Iran's squad had arrived in Australia for the tournament shortly before the war in the Middle East began on February 28, complicating travel arrangements.
Assistant Immigration Minister Matt Thistlethwaite described the women's plight in Australia as a "very complex situation".
"These are deeply personal decisions, and the government respects the decisions of those that have chosen to return. And we continue to offer support to the two that are remaining," Mr Thistlethwaite said.
The two players who stayed in Australia have been moved to an undisclosed safe location and are receiving assistance from the government and the Iranian diaspora community, he said.
Concerns about the team's safety in Iran heightened when the players didn't sing the Iranian national anthem.
The Australian government was urged to help the women by Iranian groups in Australia and by Trump.
The embassy in Canberra, remains staffed, despite the Australian government expelling the ambassador last year.
with AP
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