Firefighters tried to help the father go back into the house to rescue his son, but flames were too heavy to reach the child.
Firefighters later recovered the boy's body from a room on the first floor.
A service dog helped the daughter, who suffers from autism. It also got out safely.
The child's mother and a toddler were at the dentist when the fire broke out.
The father was recovering Friday from severe smoke inhalation and cuts he received while rescuing his daughter.
The cause of the fire is under investigation.