The bodies of the infant and the 39-year-old man were found late Sunday behind a home in the northeastern part of the city.
Montreal police spokeswoman Anie Lemieux says the boy's mother contacted police in the evening after the father failed to return with him as planned Sunday afternoon.
"When police officers got there, they searched the area and the man and the child were found in the shed at the back of the house," she said Monday.
The mother was taken to hospital to be treated for nervous shock after officers found the bodies, Lemieux said.
She also said the woman and her husband were officially separated.
"The information investigators were able to get so far is that the couple was living under the same roof, but they were (involved) in divorce proceedings," Lemieux said.
She said the father killed the child and then took his own life, but it's too early to say how that happened.
Autopsies will be necessary to determine the exact cause of the deaths, Lemieux said.