Police tracked the 56-year-old to a rural property in Thologolong, near Walwa on the Victorian-NSW border.
Freeman was wrapped in what appeared to be a blanket when he emerged from a container-like structure on Monday morning following a three-hour stand-off with heavily armed officers.
Victoria Police Chief Commissioner Mike Bush said he had viewed footage of Freeman pulling the gun from underneath the cloth and turning it towards police.
"I can now confirm that it is a police firearm, and we believe it was taken from one of our murdered officers on the 26th of August," he told reporters in Wodonga on Monday evening.
It is not known if Freeman fired the gun before multiple officers discharged their weapons.
Freeman was wanted over the fatal shootings of Neal Thompson and Vadim de Waart-Hottart, who were among a team of officers serving a warrant at his home in the small town of Porepunkah in late August.
The property is about 150km from where Freeman was shot dead.
Officers moved into position on Sunday but Mr Bush would not confirm whether they received a tip-off about Freeman's whereabouts.
Police are investigating how the fugitive evaded capture for 216 days and exploring the possibility he received help.
"We're very keen to learn who, if any, but I'm sure some, actually assisted him getting away from Porepunkah to where he was located," Mr Bush said.
Mr Bush said Freeman's appearance was slightly altered from his last confirmed sighting, fleeing into dense bushland the day of the shooting.
"His hair was a little bit longer and he had a beard," he said.
State Coroner Liberty Sanger visited the scene on Monday to formally confirm the man's identity.
The commissioner said he expected the process to take 24 to 48 hours.
"The deceased is still on site so that will take some time," Mr Bush said.
"We're confident of who that person is."
Premier Jacinta Allan rejoiced at police bringing the manhunt to a close, declaring an "evil man" was dead.
"It is over in terms of the operation but it will never be over for those families," she said.
Police Association secretary Wayne Gatt said the memories of the fallen officers would live forever.
"The memory of cowards fades quickly but with heroes it lives on forever," he said.
Hundreds of police from across Australia took part in the search for Freeman in extreme conditions, including snow and heat, and dense bushland in mountainous terrain.
Investigators in December revealed they had shifted their search efforts to locating the killer's body.
Victoria Police offered a $1 million reward and the possibility of indemnity for information leading to his capture - the largest financial offer in the state's history for facilitating an arrest.
