The Van Gogh museum in Amsterdam said the works were found during a “massive, continuing investigation” by Italian prosecutors and organised crime officials.
The paintings were taken when thieves used a ladder and sledgehammers to break into the museum.
They were eventually found wrapped in cloth in a safe in a house in the picturesque seaside town of Castellammare di Stabia, near Pompeii.
The works were among assets worth millions of euros seized from a Camorra organised crime group linked to cocaine trafficking, Italian reports said.
Months earlier, police had arrested several suspected drug traffickers who had invested their proceeds in Dubai, Spain and the Isle of Man. They were reportedly linked to one of the biggest mafia clans in the Scampia area of northern Naples.
Among those arrested in January were suspected drugs gang leader Raffaele Imperiale and Mario Cerrone. It was Cerrone who apparently told investigators about the two paintings.
Police in Naples said the paintings, which they described as “priceless”, were discovered during a raid as part of a crackdown against a Naples-based Camorra crime clan suspected of cocaine trafficking.
The paintings were seized along with other property, worth “tens of millions of euros”. The Financial Guard, a branch of the Italian police, often sequesters the financial assets of suspected criminals.
Van Gogh Museum director Alex Rueger thanked the Italian police, saying: “After all these years, you no longer dare count on a possible return.”
It is unclear when the paintings will return to Amsterdam.
The theft of the two works, valued by investigators at £77 million, led to criticism of security at the world’s major art museums.
The thieves broke into the museum through the roof during the night of 6-7 December 2002 and used sledgehammers to break a first-floor window.
They took the paintings off the walls of the main exhibition hall. Experts were baffled at the time of the theft because guards had been on patrol and infra-red security systems were in place.
Neither work was insured at the time, and both were on loan to the Van Gogh museum from the Dutch government. Two Dutch citizens were jailed for theft but always maintained their innocence.
Dutch and Italian ministers were overjoyed by the news, and praised Italian investigators.
Edvard Munch’s 1893 work The Scream was found two years after it was torn from a museum wall in Oslo in 2004
The Sc ream and a second Munch masterpiece, Madonna, were seized by armed men who raided the Munch museum in Oslo. Several men were jailed and the paintings later recovered after painstaking detective work in 2006.
Another version of The Scream was stolen from the National Art Museum in Oslo in 1994 and that too was later recovered in a sting operation by UK detectives.