The boy was unconscious and suffering from hypothermia when ambulance workers were called to the flat in the working class Saint-Josse area of the Belgian capital on Monday evening, it said.
Local media said he had been forced out onto the balcony at around 5 am the day after Christmas Day and stayed there until around 8 pm.
“The step-father has confessed without realising the seriousness of the facts, while the mother is still in denial,” the prosecutor’s office said in a statement.
Both were being held in police custody.
The balcony was at the back of the apartment building and was not visible from the street, which local media said explained why no-one had called police or emergency services sooner.
It was not immediately clear if it was neighbours or the parents themselves who finally made the emergency call.
Local authorities said the children were not registered at any school in the city.
The parents face charges of “torture of a minor by someone in a position of authority.”
Emir Kir, the mayor of the district of Saint-Josse, told RTL radio: “What is very serious and very sad is that (the apartment) is next to the offices of ONE (child welfare authority) and across the road from a police station.”