The auction house Paris Druout had expected the green-and-pink silk shoes to sell for up to 10,000 euros.
Auctioneers said they had been flooded with bids from around the world.
Other artefacts on sale belonging to the 18th Century monarch included portraits and a dinner set once owned by her husband, King Louis XVI.
“Obviously, it’s rather rare to find objects that belonged to the queen, particularly dresses or more intimate things,” said art expert Cyrille Boulay.
“I have been doing the job of historical artefacts expert for 20 years now, and it’s just the second time that I have a pair of shoes on sale.
“So it’s rather exceptional and therefore of course, it has sparked an international interest.”
The successful bid was placed by telephone but the buyer’s identity has not yet been disclosed.
Louis XVI married Marie Antoinette, daughter of the emperor and empress of Austria, in 1770 and the couple amassed an opulent collection of artwork and furniture.
The queen’s extravagant spending habits caused her to be nicknamed “Madame Deficit”.
Following the French Revolution, she was convicted of treason and guillotined in the French capital on 16 October 1793.
A fragment of a patterned silk dress she owned before her arrest was also included in the 80 lots auctioned on Wednesday, a day after the anniversary of her death.
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