Two of the medallions, made of gold foil inside blown glass, are "priceless" Jewish artifacts, said James Snyder, director of the museum. Emblazoned with lions of Judah and a seven-branched candelabra, they are among the earliest pieces found outside Israel bearing images linked to the Jewish temple in Jerusalem, he said.
All three medallions were part of a collection of thousands of antiques, paintings, tapestries and other artifacts that Countess Isabella Dzialynska amassed in the 1800s and kept at her castle in Goluchow, Poland.
The Nazis seized the collection in 1941 after invading Poland, then moved them on Hitler's orders to an Austrian castle. There, they were looted after the Nazi defeat in 1945 and scattered to museums, dealers and private collections all over the world, according to the London-based Commission for Looted Art in Europe, which represents Dzialynska's heirs. The commission approached the Israel Museum four years ago upon discovering the medallions were in its collection and negotiated the restitution agreement.
The medallions had turned up in Vienna in the 1960s and were purchased for the Israel Museum.
The family spent years "scouring Germany and Austria" for its lost art after the war, then largely stopped looking, said Count Adam Zamoyski, the countess's great-great-nephew. The search, he said, got under way again in earnest in the 1980s, when awareness of looted art became more widespread and museums became more forthcoming about such pieces in their collections.
Numerous artifacts have surfaced over the years. Most recently, a 13th-century enamel cross located in Austria was returned to the family two months ago.
The two medallions bearing the Jewish symbols will remain on display in the museum. The museum repurchased one from the heirs, and a donor purchased the second and gave it to the museum on a long-term loan.
"We absolutely decided that because they were of such extraordinary importance to the museum, we were very keen for a way to be found for them to remain there," Zamoyski said, adding he was "very pleased" with the agreement.
None of the sides would divulge the sums paid for the medallions.
The medallions were buried in Jewish graves in the catacombs of Rome in the 3rd or 4th century, said Snyder, the museum's director. The images recall the temple in Jerusalem that Roman legions destroyed in the year 70, before carrying its treasures - including a seven-branch candelabra like the one depicted on the medallions - back to Rome.
The third medallion, which bears the image of a duck and a fruit basket, is returning to the heirs.
Worldwide, experts say, anywhere between 250,000 and 600,000 pieces of art looted by the Nazis were never claimed and remain in the possession of museums, governments and private collectors. In its nine years of work, the Commission for Looted Art in Europe has restored 3,000 pieces to their owners, said Anne Webber, the commission's co-chair.
"Because for many people the loss of their art represented the loss of their lives, the lives they had, to return it to people returns something of that life to them," Webber said.
Over the years, the Israel Museum has returned some 20 pieces looted by the Nazis and claimed by heirs, including Camille Pissarro's "Boulevard Montmartre: Spring" in 2000. The original owners' heirs agreed to leave the painting on display at the museum, accompanied by an explanation of its history.