The paintings were taken when thieves used a ladder to break into the museum.
Italian police said the works were recovered from the Naples mafia.
They were among assets worth millions of euros seized from the Camorra group, reports said.
The theft of the two works, described as priceless, led to criticism of security at the world`s major art museums. Neither work was insured at the time, and both were on loan to the Van Gogh museum from the Dutch government.
The museum said it was so far unclear when the works would be returned to Amsterdam but in a statement it said they appeared to be in "relatively good condition".
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