The recovery of Zachary Baumel's remains closed a famous case that has plagued Israel for nearly four decades, but Israeli officials have declined to elaborate on how the return was arranged or where the remains were found.
The Israeli spokesman who announced it on Wednesday only said that "an opportunity arose to locate the body" through an unnamed country.
Baumel went missing in a 1982 battle with Syrian forces in southern Lebanon along with five other Israeli soldiers. Several years later, two of the missing soldiers were returned alive to Israel in prisoner exchanges with Syria, but the fate of the other three had remained unknown.
A Syria-based official with a Palestinian militant group told The Associated Press on Wednesday that insurgents who were in control of the Palestinian refugee camp of Yarmouk in the capital, Damascus, up until last year excavated graves in search of the remains of the three missing soldiers.
Speaking on a visit to Moscow Thursday, Israeli Prime Minister Benjamin Netanyahu thanked Russia for its assistance in finding the remains, and Putin acknowledged that Russia had worked to retrieve them.
"Our military together with Syrian partners established the place of his burial," Putin said at the start of the meeting. "We are very pleased that at home they can give him the necessary military honors."
Syria, however, released a statement Thursday denying any knowledge of the remains.
"We have no information on the entire matter of the remains or whether any such remains exist," the statement published on state-run news agency SANA said. It said Israel's recovery of the remains is new evidence that confirms cooperation between "terrorist" groups in Syria and Israel's Mossad spy agency.
Public involvement in the return of the remains to Israel would be embarrassing for the Syrian government, which is technically at war with Israel.
Baumel's burial ceremony, held at Mount Herzl in Jerusalem, Israel's national cemetery, drew thousands of Israelis Thursday. Fresh off the plane from Moscow, Netanyahu attended and addressed the crowd.
"I felt a shudder when I was told that Zechariah will be with us again," he said. "We will be able to pay our last respects. We waited 37 years for this moment."
Cases of missing soldiers have a powerful emotional and political resonance in Israel, where military service is compulsory for most Jewish men. Netanyahu lauded the repatriation of Baumel's remains as an "expression of mutual responsibility and feeling of unity" that he said epitomizes Israel.
Putin's foreign affairs adviser Yuri Ushakov told journalists the two leaders discussed events in Syria but that Netanyahu did not present any concrete plan for regulating the conflict and tensions there.
Israel and Russia have a military hotline to coordinate air force operations over Syria, where Russia supports President Bashar Assad's forces and Israel frequently strikes targets linked to Iran and the Lebanese Hezbollah.