In a unanimous decision, the Federal Court found the man's application for refuge hadn't been considered fairly.
His deportation to Kabul is on hold and it appears his application will now be reconsidered.
Refugee advocates say the case will have ramifications for more than 100 asylum seekers.
Reporter: Samantha Donovan
Speakers: Pamela Curr, Asylum Seeker Resource Centre; Victor Harcourt, Russell Kennedy law firm
SAMANTHA DONOVAN: The supporters of the asylum seeker known to the court as 'SZQRB' say he was persecuted in his homeland and made a scapegoat by the Australian Government.
Pamela Curr is from the Asylum Seeker Resource Centre.
PAMELA CURR: He's a simple Hazara man who was victimised because of his religion and his ethnicity. In Afghanistan today, the Hazaras are being massacred. They're being massacred in Pakistan where they've fled to.
This man has a wife and children left behind. The day he was picked up and put back in detention he was tiling the bathrooms of Melbourne. That's what he does. He works, 12, 14 hours a day, laying tiles. And the Immigration Department have decided to make him, to try and send him back as a victim. Well they failed.
SAMANTHA DONOVAN: In September last year the man was due to be deported to Kabul after his application for asylum had been rejected. The matter was referred to the then minister for Immigration Chris Bowen. He had the discretion to consider granting the man a visa if he considered it to be in the public interest. Mr Bowen declined to consider the case.
Lawyers for the asylum seeker argued his decision was procedurally unfair. Today the Federal Court accepted that argument. It found that Minister Bowen decided to deport the man regardless of whether the assessment of Australia's treaty obligations was factual or legally correct and even if his view that Australia didn't owe the man protection was wrong.
Pamela Curr from the Asylum Seeker Resource Centre says the man wasn't given a fair go. And that the Federal Government had set up a system to handle the cases of asylum seekers arriving by boat differently to other applicants.
PAMELA CURR: It was designed to exclude people rather than to examine their cases fairly and accept them. And that's what happened. This man is one of 120 that we know the department and the Minister have marked for removal. Today, justice triumphed. He's not going anywhere at the moment. And we hope that they don't appeal it to the High Court.
SAMANTHA DONOVAN: The asylum seeker wasn't brought into court in time to hear the decision. He was briefed by his lawyers afterwards. Victor Harcourt is from Russell Kennedy.
VICTOR HARCOURT: We're delighted that five out of five judges of the Federal Court have agreed with our submissions that our client's claims were not assessed according to law. And what it means is that our client can now make his application to be assessed. And to have it decided according to the law. So for him, he gets another opportunity.
SAMANTHA DONOVAN: Pamela Curr says today's Federal Court decision will have ramifications for more than a hundred other asylum seekers with pending claims.
PAMELA CURR: These guys' cases, and I've got a box of them on my desk, are no different to the cases of the people who are granted refugee visas and who are living and working in Australia today.
These 120 were victims, effectively, of a system. A flawed system. And this Government has been dead keen to send them back to Afghanistan in order to send a message. A message to tell people not to catch the boats.
The average Australian doesn't understand this. It's complicated legal stuff to them. But it's life and death. What we were talking about today was a man being loaded on a plane, sent back to Kabul. He would get off that plane and he would be marked. And he would surely be killed. Now, that's been stopped. And we've got to stop it for the other 120.
SAMANTHA DONOVAN: How would you describe his reaction to the news?
PAMELA CURR: He's a working man. He doesn't have much English. He said through the interpreter 'I am proud and I am calm and I'm thankful'.