One was taken to hospital by helicopter and is in a serious condition. The second man is considered stable.
A Victoria Police spokesman said detectives were still establishing exactly what happened during the break-in.
Monday’s incident is the latest in a string of aggravated burglaries across Melbourne that have left residents in some suburbs fearful that their home might also be targeted.
Early on Sunday morning, a family of six, including three children,hid in terror in a bedroom as a gang burgled a Springvale house.
Police believe four or five offenders broke a front window of the Heather Grove home at about 1.45am.
A man who heard the break-in fled to a rear bedroom with his wife, three children and father-in-law, locked the door and huddled there until the thieves drove off in the family’s two cars.
Victoria Police set up Operation Cosmos in May in response to the rise in aggravated burglaries and carjackings.
On Sunday, the taskforce charged two teenage girls in relation to a string of offences in Melbourne’s south-east, including aggravated burglary, robbery and theft.
The two 16-year-olds, one from Cranbourne North and the other from Pakenham, were arrested in an alleged stolen car in Dandenong.
The girls had allegedly committed the offences in Berwick, Dandenong, Lynbrook, Drouin and Longwarry over the past two months.
Last week, police charged two teenage boys – a 17-year-old from Taylors Hill and a 14-year-old from South Yarra – with aggravated burglary and theft of a motor vehicle.
The incidents are alleged to have occurred at a property on Shoalhaven Drive, Caroline Springs last Saturday and a property on Wellesley Drive, Taylors Lakes, last Sunday.
Since the launch of Operation Cosmos there have been almost 80 arrests.