The books were confiscated from a German auction house in 2012, leading to the arrest of the auction house director, Herbert Schauer.
Set to collect their missing books is the Girolamini Library in Naples. The books were slowly removed from the collection by the library's former director Marino Massimo De Caro, who was sentenced to seven years in prison for the thefts.
A spokesman for the Bavarian State Prosecutor's office told The Local that the books have been in their possession while ownership could be established.
"There are several books here and we had to go through each one individually to establish ownership, though our findings did prove that the Girolamini Library was indeed the rightful owner of all 543 books," he said.
The books include dozens of titles by Italian physicist Galileo Galilei and Renaissance astronomer Nicolaus Copernicus as well as German astronomer Johannes Kepler. Most of the titles are books from the 16th and 17th centuries.
The books came to Germany through a sale to Zisska & Schauer, which now is known as Zisska and Lacher.
"We had been looking at the books for months," auction house owner Wolfgang Lacher told DPA. "They were brought to us under false pretences and registered as part of the estate of a couple from northern Italy."
The Munich prosecutors noted that the auction house was fully cooperative once the books actual pedigree was known.
Schauer was sentenced to five years in prison in Italy for the theft, though his sentence is still pending appeal.
De Caro stole the books over a four-month time period in 2012. In April, the library announced around 1,500 books were missing.
It is now up to the Italian authorities to decide how the books will be transported.
The Girolamini library belongs to the church and convent of the same name in Naples. The collection started in the 16th century and has become one of the most important literary collections in the world.
By Sabine Devins
With reporting by The Local Italy's Rosie Scammell.