Detective Inspector Al Hanson told media today he believed the offenders fired a number of shots from the road or footpath towards the home in Endeavour Hills about 1.20am.
The 17-year-old boy was rushed to The Alfred hospital in a stable condition, where he remains.
Other family members, who were home at the time, were not injured.
Police said the shooting appeared to be a targeted attack, although believe the occupants of the home, including the teenage boy, were not the intended target.
He said it was “extremely lucky” the teenage boy survived.
Investigators are now reviewing CCTV footage of a car seen to be circling the home moments before the shooting.
“There is nobody at the address that we think is the target,” Hanson said.
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“CCTV collected and witnesses in the street at the time have said a vehicle had done a couple of laps of the court.
“They specifically stopped outside of the address and fired shots.
“No other houses or cars were imparted by the rounds fired by the offenders.
“We believe two rounds were fired through the window.”
Police are also probing whether a burnt-out Mitsubishi Eclipse found at a reserve in Narre Warren is linked to the shooting.
“It was stolen from a property in Mornington in August and we have information that suggests the burning out of the vehicle may resulted in injury to one of the people involved,” Hanson said.