Wanted for a string of property and violent crimes, they evaded capture despite multiple sightings until a tip-off led heavily armed police to a farm in Dunedoo, 345 kilometres (213 miles) northwest of Sydney.
No shots were fired. Both men suffered minor injuries as they resisted arrest.
New South Wales Police Assistant Commissioner Clint Pheeney said the body found after the arrests was believed to be that of a 68-year-old man missing since October 8.
"Overall, this has been a very intense operation which has spanned a number of states," he added, as a murder investigation was launched.
The pair had been criss-crossing between New South Wales and Victoria states for the past 12 days, with police warning they were armed and dangerous.
Pheeney defended the time it took to capture the men, who were suspected of having stockpiles of supplies and weapons along their route.
"If we look at how these people operated and if we look at the expanse of country out here, the number of roads that are sealed, unsealed, back roads, forestry trails, these people knew the bush," he said.
"They knew the bush very well, they knew all the ways and times to avoid police."
The men have yet to be charged but police earlier said they wanted to charge Gino, 58, and Mark, 35, with 13 offences each, including attempted murder.
Both men have reportedly spent time in prison for crimes going back at least as far as 2004, when Mark assaulted his mother.
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