The two 16 year olds were arrested on Thursday following an investigation into the death of 33-year-old GP Ash Gordon in Doncaster on Saturday.
Police found Dr Gordon on Eildon Street about 5.30am after responding to reports of an aggravated burglary at his Sargent Street home. He died at the scene.
Police allege he was fatally injured in a confrontation with the offenders.
Serious Crime Division Superintendent Janet Stevenson said in a statement that investigators had worked tirelessly to identify and apprehend those responsible.
"We know that Ash's family and loved ones are grieving. 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.
She said Dr Gordon was a much-loved and valued member of the community.
"This type of incident can create fear and uncertainty," Supt Stevenson 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."
The two teens have been charged with murder, aggravated burglary and theft, and will appear at a children's court at a later date.
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