Emergency services rushed to free the trapped 47-year-old from the wreckage, which was lying on the roof of a home in Tylden Court in Mentone.
The Mount Martha man was taken to the Alfred Hospital in a stable condition with lower body injuries after being taken off the roof on a stretcher with a crane.
He was the only person in the helicopter when it crashed just after 1pm.
The student was conducting a navigation flight on return to Moorabbin Airport when the chopper came down.
The homeowner, a woman in her 80s, was at Bunnings at the time.
The damage was confined to a bedroom and bathroom of the house, which is is less than 1km from Moorabbin Airport.
Australian Transport Safety Bureau Chief Commissioner Angus Mitchell has said the Hughes 269C helicopter crashed when it was conducting “a missed approach (go-around) procedure from Moorabbin Airport”.
“As part of its investigation, the ATSB will interview the pilot and any witnesses, and obtain and review recorded data, weather information, aircraft information and maintenance records,” the spokesperson said.
“The ATSB will publish a final report, detailing contributing factors and any identified safety issues, at the conclusion of the investigation.
“However, should any critical safety issues be identified at any stage during the course of the investigation, the ATSB will immediately notify relevant parties so appropriate safety action can be taken.”
An assessment of the safety of the house is also underway.