Ms Murphy's body still has not been found and the search for her is ongoing.
Five weeks after she vanished, having set out to go for a run from her Ballarat East home, police on Thursday charged the 22-year-old with her murder at Mt Clear.
He appeared in Ballarat Magistrates Court on Thursday afternoon.
"We are alleging a deliberate attack that has caused the death of Samantha," Chief Commissioner Shane 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.
Samantha Murphy's husband Michael said the Ballarat community had rallied around his family. (James Ross/AAP PHOTOS)
Ms Murphy, a mother of three, has not been seen since February 4.
Her husband Michael told reporters he was relieved.
He described the past few weeks as "sh**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; it hasn't been a good nearly five weeks," he said.
Mr Patton commended Ms Murphy's family for withstanding the scrutiny they have been under since the investigation was launched and thanked all the 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 were involved in the probe.
Anyone who has information, including CCTV or dash-cam footage from the time she 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 was launched around Ballarat after Ms Murphy disappeared, which involved both trained emergency services workers and hundreds of concerned locals.Â
They combed dense bush, private land and walking tracks.
Buninyong Police Station, which was originally a base for the operation, was unattended on Thursday with the lights off and 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 smartwatch 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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