The teens were arrested on Thursday, following an investigation into the death of Ash Gordon, 33, in Melbourne's northeast on Saturday.
Dr Gordon was found on Eildon St in Doncaster about 5.30am by police who were responding to reports of an aggravated burglary at his Sargent St home.
Police will allege he was involved in a confrontation where he was injured and died at the scene.
A 16-year-old Dandenong boy and 16-year-old Travancore boy were charged with murder, aggravated burglary and theft after being interviewed by police.
The teens faced a children's court on Thursday afternoon, when they were brought into court flanked by three police officers.
The boys stared straight ahead and remained silent during the brief hearing as further court dates were set.
There was no application for bail. One of the boys' lawyers said it was his first time in custody.
The other boy had refused to allow his parental guardian to be present when he was interviewed by police, a prosecutor told the court.
The prosecutor said police were combing through CCTV footage, analysing phones and awaiting forensic analysis.
She requested 12 weeks to compile a brief of evidence.
The prosecution is also seeking parental approval to obtain DNA from the two boys, the court was told.
The accused teens were taken back into custody and will return to court on February 8 for the forensic application.
They will then return for a committal mention on May 23.
Earlier on Thursday, Serious Crime Division Superintendent Janet Stevenson said Dr Gordon was a much-loved and valued member of the community.
"This arrest will not take away the tragedy of this dreadful situation, but we hope that it will alleviate some of their distress," she said.
"We want our community to feel safe in their homes and to that end, Victoria Police will continue to do everything in our power to make this a reality."
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