Australia had granted humanitarian visas to six players and one support staff member after they sought asylum, saying they feared possible persecution if they returned to Iran.
Concerns over their safety surfaced when several players failed to sing the national anthem at a women's Asian Cup match earlier this month after the United States and Israel launched the war against Iran.
Iranian state television had labelled them "wartime traitors". The team, which flew into Istanbul on Tuesday, took a flight to Igdir in eastern Turkey on Wednesday morning.
The players emerged from Igdir Airport pulling their luggage and chatted in front of the terminal before boarding a bus to the border. One of them briefly smiled and waved at a TV camera before the bus departed. After a trip of around two hours to the frontier, they went through passport control at the Gurbulak border gate before crossing over into Iran.
The team's Asian Cup campaign began just as the United States and Israel launched strikes on Iran, killing Supreme Leader Ayatollah Ali Khamenei.
They were eliminated from the tournament more than a week ago. Five of those who had sought asylum in Australia subsequently changed their minds and decided to return home, with Australian media reporting the latest withdrawal on Monday.
They rejoined the rest of the squad in Kuala Lumpur, where the team had been staying since leaving Sydney last week.
The Iranian Football Association (FFIRI) said last week those who had changed their minds would travel home with the rest of the team "to once again be embraced by their families and homeland."
Two players are still in Australia and have been pictured training with a local A-League club.
