A court in the city of Lille had ruled they should be allowed to remain open in August
Overturning a lower court decision in favour of the shop owners, the Council of State ruled their premises were "unhygienic" and a "serious fire hazard".
In its ruling it backed the authorities' claim that the shops and cafes were being used for smuggling activities that had "caused tension and violence."
The decision comes as the state prepares to dismantle the camp in northern France where between 7,000 and 10,000 migrants live crammed in tents in squalid conditions.
Asylum seekers are to be moved to shelters around the country.
Many shops and cafes in the camp had already closed.
In August, a court in the city of Lille had ruled they should be allowed to remain open, saying they fulfilled an important social role for the migrants.
Calais is a magnet for migrants trying to reach Britain by stowing away on trucks heading across the Channel from France.
Around 1,000 unaccompanied minors are among those living in the "Jungle".