The child was forced to stay outside the flat in the Saint-Josse area of the capital from 5 a.m. to 8 p.m. Monday after helping himself to something to eat from the kitchen, Het Laatste Nieuws newspaper reported.
Emergency services found the little boy "unconscious and suffering from hypothermia and malnutrition," the Brussels prosecutors office said in a statement, adding that he was "still in a very critical condition."
His twin sister was also taken to hospital suffering from mistreatment and malnutrition.
The children's mother, 31, and their 21-year-old stepfather have been arrested on suspicion of "torture of a minor by someone in a position of authority," the Brussels prosecutors office said.
"The step-father has confessed without realizing the seriousness of the facts, while the mother is still in denial," the prosecutor's office said.
The woman is a French national while the step-father is Belgian, Het Laatste Nieuws reported.
Neither child was registered in Belgium, making it more difficult for authorities to monitor their welfare, local mayor Emir Kir told RTL-TVI television.