The positive identification follows forensic testing carried out on the body found in bush 52km from the site where Ms Ristevski was last seen.
The news answers part of the question of what happened to Ristevski, but there are plenty more questions as homicide detectives and forensic police investigate.
Ristevski, 47, vanished nearly eight months ago and her remains were found less than 30km north of Toolern Vale, where a two-day search for Ristevski was centred two months ago.
On December 19 and 20 last year, police drained dams and searched countryside south of the bushland where the body was found on Monday.
It was a case that gripped Victoria from the moment Ristevski left her $1.1 million home in Avondale Heights, in Melbourne's north west, on June 29, 2016, and disappeeraed without a trace.
Her husband, Borce Ristevski, said his wife went for a walk to "clear her head" after an argument over finances and reportedly told family she may have been snatched by a stranger.
As Missing Person Squad detectives collected hundreds of hours of footage, police theorised she had met with foul play.
It was revealed on Tuesday that a witness told police he saw a man with a shovel at the location where Ristevski's body was found.
The witness allegedly joked "What did you do to the body?" to the man but was met with an expressionless face, the Herald Sun reports.
Local resident Ian Flannery told 9 News he "could not believe" the grisly find near a quiet cul-de-sac.
"I'm a bit flummoxed. It's very, very unusual," he said.
Police conducted a line search at the scene on Monday and are keen to speak to anyone that may have seen any suspicious activity in that area.
"Missing Persons Squad detectives are appealing for anyone that may have been walking along the dirt track off Loch Road or anyone that may have seen any vehicles to contact them," police said on Tuesday.
Investigators are also hoping to speak to anyone that may have been at Mount Macedon any time from June last year and took photos or any video footage in the area.
On Monday, Karen's nephew, Chris Ristevski, was stunned when told by the Herald Sun of the discovery of the body.
"I'm shocked, I haven't heard anything about this so I'm still trying to take it all in," he said.
The remains were found less than 30km north of Toolern Vale, where a two-day search for Ristevski was centred two months ago.
