The extraordinary story of an ancient wine cup that was awarded to the marathon winner of the first modern Olympics before being smuggled out of Greece by a notorious Nazi has been brought to light after its return to Athens.

The 6th century BC pottery vessel was bestowed upon Spyros Louis, a water carrier, when he unexpectedly won the inaugural marathon in 1896. Then it went missing.

Georgios Kivvadias, director of the vase collections at the National Archaeological Museum in Athens, said: “In 2012, when asked to investigate what had happened to it, I began checking bibliographies and archives. It was thought it was inventoried in our archives but that wasn’t the case at all.”

What followed were two years of detective work before the archaeologist eventually found the vessel, decorated with an image of two black-figured athletes against a clay-red background, at the University of Münster, in Germany.

The double-handled cup – originally discovered in a tomb in Thebes – was acquired by the university in 1986.

On Wednesday the cup was formally repatriated in a handover ceremony at the museum, where the university’s rector spoke of the “bittersweet” experience of giving it up, and Greece’s culture minister, Lina Mendoni, spoke of the gratitude of the Greeks for getting it back.

“The noble gesture of the university of Münster is a very important gesture of the German people to the Greek people,” she told an audience gathered at the museum. “Cultural heritage belongs to the people who created it.”

How the ancient vase got to Germany may have played no small role in the university’s decision to hand it back.

Kivvadias said: “After Louis was handed the pottery, it disappeared until 1934 when it re-appeared in the hands of Werner Peek, an archaeologist who had won a grant to work at the German Archaeological Institute in Athens. Peek had amassed a collection of antiquities during his time here in the thirties and probably bought it on the art market in Athens.”

The connoisseur of ancient artworks and respected classical philologist was also an ardent Nazi sympathiser and antisemite.

Peek later confessed he handed his entire 68-strong collection to Hermann Göring, the notorious Nazi military leader, when he paid a visit to Athens in 1934 – seven years before the Wehrmacht occupied Greece.

Göring, one of the architects of the Third Reich police state and later associated with the plundering of Jewish treasures, concealed the antiquities in diplomatic pouches.

“The cup was smuggled out of the country with the rest of his collection by Göring,” Kivvadias told the Guardian. “Then when [Peek] returned in 1937 it ended up with him in East Germany, where he lived for years, was allowed to travel freely and taught as a professor.

“It was only when he went to the West in the late 1980s that he decided to sell the collection to the University of Münster, which acquired it without knowing the exact origins of the pieces.”

At a time when Athens has stepped up its campaign to retrieve the Parthenon marbles from the British museum – ahead of the nation’s bicentennial independence celebrations – the repatriation of the cup could not be more timely.

The vessel, currently on display in the National Archaeological Museum, will remain in Athens until early next year, when it will be exhibited at a museum chronicling the history of the Olympics in ancient Olympia, the birthplace and venue of the original games.

Dr Erofili Kollia, the director of the Archeological Museum of Olympia, said: “It will have pride of place here. The piece is hugely significant both as an artwork whose value is undisputed and because it was given to Louis, the victor of the first marathon when the modern Olympic games were revived. We are overjoyed that it will be here, with us, again.”