Boochani won $17,000 with the award, which is Australia's richest prize for biographical writing, organisers at the State Library of New South Wales said in a statement on Monday.
Boochani has already won several other prizes this year, including the Victorian Premier's Literary Award, the New South Wales Premier's Literary Award, and non-fiction book of the year at the Australian Book Industry Awards.
In his memoir, Boochani details his journey after leaving Iran, arriving from Indonesia to Australia's Christmas Island on a boat, and being imprisoned by the Australian government on Manus - where he has been held for more than six years - with some shocking details of cruelty, humiliation and constant surveillance.
Boochani attempted to reach Australia by boat from Indonesia twice, Al-Jazeera News Agency reported.
On the first attempt, the boat sank and Boochani was rescued by Indonesian fishermen.
In July 2013, his boat, which held 75 asylum seekers, was intercepted by the Australian Navy and he was transferred to the Manus Island detention centre.
Manus is a territory belonging to Papua New Guinea but has been used by Canberra since 2013 as a place to send asylum seekers who try to reach Australia.
The practice has been denounced as contravening the human rights of the refugees and migrants detained there.
Boochani wrote his book one text message at a time from Manus. It was translated from Persian into English by a friend.
The judges on Monday praised the book for "its poetic and epic writing", calling it "profoundly important, an astonishing act of witness and testament to the lifesaving power of writing as resistance".
Boochani, unable to accept the award in person, thanked the organisers and his supporters through a phone messaging app from Manus Island.
"I think history will judge this generation and will judge all of us in this hard and dark period of Australian history," he said.
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