The men were not charged with organising the people-smuggling venture or with the deaths of any passengers who perished when the boat sank off Christmas Island in June 2012.
Boy Djara, thought to be aged 26 or 27, was effectively second in charge on the boat which was crammed with more than 200 asylum-seekers mostly from Pakistan and Afghanistan when it sank.
He was found guilty of six counts of people-smuggling in Perth District Court and sentenced to nine years in jail, with a non-parole period of six years, a court official confirmed.
He will be eligible for parole after four years.
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Scores of asylum-seekers have drowned when their boats foundered en route to Australia in recent years, most of them having paid people-smugglers to bring them on wooden vessels from Indonesia.
In the incident in June 2012, the small wooden fishing boat started taking on water and eventually capsized about 200 kilometres (124 miles) from Australia's Indian Ocean territory of Christmas Island.
In sentencing, Judge Patrick O'Neal said the vessel was overloaded and carrying life jackets which were not suitable for the open sea.
"If sheep or cattle had been transported like this, people would have rightly lined the wharves... To protest," O'Neal said in sentencing comments reported by the Australian Broadcasting Corporation.
Australia tightened its rules regarding asylum-seekers following a series of sinkings, with those arriving by boat now refused resettlement in Australia and sent to Papua New Guinea or Nauru.
In July 2013, unrest rocked the centre in Nauru, causing Aus$60 million (US$55 million) in damage and prompting charges against 63 asylum-seekers.