Keen-eyed experts snapped up a handful of the coins, which were struck in gold, silver and bronze by the Italian mint, before the mistake was noticed.
Vatican coins and medals bearing the face of Pope Francis are bought by collectors all over the world.
A few collectors may make a fortune because of the scarcity value of the flawed medals, the BBC’s David Willey reports from Rome.
New medals are struck when every new pope is elected and they provide a useful source of income for the Vatican, which is undergoing a major spending review under the leadership of Pope Francis, our correspondent says.
As news of the mistake travelled, social media users cracked jokes about this new religious figure, “Lesus” Christ. “I blame the Lesuits,” went one tweet while another had “Let us prey Lesus”.