Ms Murphy's body has not been found, with the search for the 51-year-old ongoing.
Five weeks after she vanished, having set out to go for a run from her Ballarat East home, police on Thursday charged a 22-year-old man with her murder at Mt Clear.
Chief Commissioner Shane Patton said the man, who is the son of a former AFL player, has not disclosed the whereabouts of Ms Murphy's body.
He appeared in Ballarat Magistrates Court on Thursday afternoon where his name was suppressed.
"We are alleging a deliberate attack that has caused the death of Samantha," Mr Patton told reporters.
Detectives from the missing persons squad arrested the man, who is not linked to the Murphy family, at his home about 6am on Wednesday.
Police are not looking for anyone else at this stage in connection with the homicide.
Ms Murphy, a mother of three, has not been seen since February 4.
Her family was told of the arrest on Wednesday night and informed of the murder charge on Thursday afternoon.
Samantha Murphy's husband Michael said the Ballarat community had rallied around his family. (James Ross/AAP PHOTOS)
Her husband Michael told reporters he was relieved.
He described the past few weeks as "s***house" and was emotional as he said the community had rallied around his family.
"It's like someone's let the pressure valve off sort of thing," he said.
"It hasn't been a good nearly five weeks."
Mr Patton commended Ms Murphy's family for withstanding the scrutiny they had been under since the investigation was triggered and thanked volunteers who had helped with the search.
"Samantha's disappearance had a profound impact on the Ballarat community," he said.
"Some cases, some disappearances, some murders, bring out outpourings of grief and we have seen that here."
Counter terrorism police, the missing persons squad and other specialist officers have been involved in the probe.
Anyone who has information, including CCTV or dash-cam footage from the time Ms Murphy went missing, has been asked to come forward.
The Ballarat area has been extensively searched for weeks but no trace of Ms Murphy has been found. (James Ross/AAP PHOTOS)
Weeks of extensive searching were launched around Ballarat after Ms Murphy disappeared, with trained emergency services workers joined by hundreds of concerned locals.Â
They combed dense bush, private land and walking tracks.
Buninyong Police Station, originally a base for the operation, was unattended on Thursday with the lights off and the door closed.
A whiteboard with a map showing where the public could help look was long gone and a sign on the door instructed anyone with information to contact Crime Stoppers.
Ms Murphy had been described as mentally and physically fit and was training for an upcoming race by doing 15km runs.
Detectives have been working with telecommunications technicians to track the route she travelled after confirming she had a smart watch and phone with her.
The Murphys have a car repair business called Inland Motor Body Works at Delacombe, a few suburbs from their home.
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