Speaking at talks with Netanyahu in Moscow, Putin was cited by Russian news agencies as saying that it had been a tough task to locate his remains.
"Our soldiers together with Syrian partners established his resting place. We are very happy that they will be able to give him the necessary military honors at home," Putin was quoted as saying.
Netanyahu thanked Putin for his country's efforts that culminated in the finding of Baumel's remains: “Two years ago I turned to you with a personal request – that you help us in finding the remains of our soldiers, including Zachary Baumel, out of the great shared values of comrades-in-arms and fellowship of soldiers,” said Netanyahu.
“You responded immediately. You said that you would act personally. You called on your people who did exceptional work,” the prime minister said.
Baumel immigrated to Israel with his parents from New York in 1970. His disappearance during the First Lebanon War, along with two other soldiers who fought in the Battle of Sultan Yacoub, has long troubled Israel.
Netanyahu made a televised statement Wednesday in which he called the mission to retrieve Baumel's remains the essence of the Israeli spirit.
"This is one of the most moving moments of all my years as prime minister of Israel," he said.