Police charged Joel Roberto, 27, and Ravyn Colley, 24, on Thursday.
Police responded to a call at a residence in a townhouse complex in the Finch Avenue and Leslie Street area of North York around 2 a.m. Monday.
Emergency services personnel informed police that a boy "with obvious injuries and without vital signs" was in the house, according to a police statement.
He was pronounced dead at the scene.
The couple made a court appearance on Thursday.