The six Gothic windows were thought vanished or destroyed until 2005, when they were discovered at Moscow's Pushkin Museum. It took another three years of wrangling before the 14th century relics, the last of 117 windows that were carted to Moscow by the Red Army in 1945, could be restored to the Church of Our Lady in the city near the Polish border.
The 48-by-84-centimetre (19-by-33-inch) panes representing scenes from the Old Testament were delivered by German Culture Minister Bernd Neumann and the Russian ambassador to Germany, Vladimir Kotenev.
At a ceremony marking the occasion, Neumann said the restitution was a sign of improving relations between the wartime foes.
"Now that the last of the 117 windows from the Church of Our Lady can finally return to their proper place, it is a further sign of reconciliation and the friendship between our two countries, between Germany and Russia," he said.
Kotenev noted that Nazi Germany had been guilty of wanton looting during the war and stressed that the process of restoring property to its rightful owners must be mutual.
"I would like to stress the word 'mutual' because there are still harsh critics and the issue of looted art is often treated in the media as one in which it is the Russians who owe a debt," he said. "It is often carelessly - or intentionally - forgotten that during the raids of the Wehrmacht many Russian museums were systematically plundered."
The windows had been removed from the Church of Our Lady during the war to protect them from bombing. But the Soviet Union claimed them as war booty and spirited them back to Russia.
After protracted negotiations, 111 panes were returned by Russia in 2002, restored in Germany and reinstalled at the church. After the final six windows are restored, they will be installed in the sanctuary's chancel.
Disputes over art treasures seized during and after the war have marred German-Russian relations since the fall of the Berlin Wall in 1989. Russian deputies passed a measure in 1997 declaring artwork seized from Germany to be rightful spoils of war to compensate for the sacking of its own collections. But Germany has refused to relinquish its claims.