Police say emergency services were called to the home at about 3:30 p.m. ET Monday regarding several people who were feeling ill.
A 52-year-old man and his 72-year-old mother were rushed to Lakeridge Health Bowmanville but did not survive. Their names have not been released.
Police say a gas-powered generator was running in the garage to supply electricity to heat the house, and although there was no access to the house from the garage, the dangerous fumes still got inside the home.
In Toronto alone on Monday night, 11 people were taken to hospital showing signs of carbon monoxide poisoning.
Capt. David Eckerman says firefighters received 41 calls for carbon monoxide, including one case in which people were using a charcoal barbecue to provide heat.
In another case, Eckerman told radio station Newstalk 1010, someone was burning furniture in a fireplace and another call was for a gas-powered generator that was in a garage seeping carbon monoxide into a home.
Police say running a gas generator, barbecue or a similar device too close to a residence can lead to carbon monoxide poisoning.