Immigration Minister Tony Burke said the women "were moved to a safe location" by Australian police. He said other squad members had been told they were welcome to stay in the country.
The women had been due to fly home, bu
t supporters had raised fears for their safety after the team declined to sing the national anthem ahead of their match against South Korea last week.
This prompted criticism in Iran, with one conservative commentator accusing the team of being "wartime traitors" and pushing for harsh punishment.
The remainder of the team was taken to Gold Coast Airport and was expected to fly to Sydney on Tuesday evening local time.
The team's coach was briefly stopped by dozens of activists who tried to persuade the other players to stay in Australia. Some protesters lay on the ground in an attempt to block the coach from moving forward. The players watched from inside the bus.
Australia's humanitarian visa programme grants permanent protection to refugees and people in humanitarian need. Visa holders can live, work and study in the country.
Speaking early on Tuesday, Burke said the five players were happy for their names to be confirmed as Fatemeh Pasandideh, Zahra Ghanbari, Zahra Sarbali, Atefeh Ramazanzadeh, and Mona Hamoudi.
"They want to be clear they are not political activists. They are athletes who want to be safe," he said, adding that talks had been going on over several days.
Giving further details, Burke said in parliament that a police officer had been inside the team's hotel and made efforts to create "the maximum amount of opportunities" for players to seek help.
The players were reportedly not able to walk around the hotel unaccompanied and were escorted to a conference room to eat meals, according to a source who spoke to SBS News.
Giving further details, Burke said that on Monday it became clear that five of the players "wanted to be able to stay in Australia".
The group left their hotel the same day and were moved to a safe location by police.
Shortly after they left, the BBC witnessed some of their minders running across the hotel to try to find them – but they had already gone.
Burke said he met the women at the safe location and then signed off for their applications for humanitarian visas - a process completed at about 01:30 local time on Tuesday (15:30 GMT Monday).
It is unclear what repercussions there might be for the players' families as a result.
"I say to the other members of the team, the same opportunity is there. Australia has taken the Iranian women's soccer team into our hearts. These women are tremendously popular in Australia.
"But we realise they are in a terribly difficult situation with the decisions that they're making," Burke said.
Australian Home Affairs Minister Tony Burke with the five players who have been granted humanitarian visas
The Iranian players' situation had earlier come to the attention of US President Donald Trump, who had taken to his Truth Social platform to demand action, saying Australia should "give asylum" to the women or "the US will take them if you won't."
Around an hour later, Trump posted again to say he had spoken to Albanese, writing: "five have already been taken care of, and the rest are on their way".
Iran was playing in the AFC Asian Cup tournament in Brisbane on Sunday, where they played against the Philippines.
Unlike their earlier match against South Korea, where the players declined to sing the national anthem, Sunday's match saw the players sing and salute during the anthem. They had also done this in their second match against Australia.
Their actions led critics to believe they had been forced to take part by government officials accompanying them during the tournament as part of the delegation.
On Sunday, hundreds of members of Australia's Iranian community - who had come to support the team in the stands - booed and jeered at the anthem, which they do not recognise.
Midway through the first half, many also unfurled the Lion and Sun flag, which served as the official state flag before the Islamic revolution in Iran. These had been snuck into the stadium in defiance of signs outside which said only Iran's current official flag could be displayed.