A White House official said Putin and Obama, who had avoided contact with the Russian leader while the two were in Paris on Thursday—also spoke to each other before the lunch.
"It was an informal conversation - not a formal bilateral meeting," White House deputy national security adviser Ben Rhodes said by email, adding the encounter lasted 10-15 minutes.
World leaders and veterans paid tribute to soldiers who fell in the liberation of Europe from Nazi German rule, at a series of ceremonies around the Normandy beaches where allied forces landed 70 years ago on June 6, 1944.
Wreaths, parades and parachute-drops honored history's largest amphibious assault, in which 160,000 U.S., British and Canadian troops waded ashore to confront German forces, hastening its defeat and the advent of peace in Europe.
Flanked by stooped war veterans, some in wheelchairs, Obama earlier joined Hollande to commemorate victory and reaffirm U.S-French solidarity before the 9,387 white marble headstones of fallen U.S. soldiers at the Normandy American Cemetery.
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It will be the last major commemoration for most of the veterans, most of whom are in their late 80s and 90s.
Obama said the 50-mile (80 km) stretch of Normandy coastline—where allied soldiers landed under fire on beaches codenamed Omaha, Utah, Gold, Sword, and Juno—was a "tiny sliver of sand upon which hung more than the fate of a war, but rather the course of human history."
"Omaha—Normandy—this was democracy's beachhead," said Obama. "And our victory in that war decided not just a century, but shaped the security and well-being of all posterity."
The president sought to link the sacrifices of World War Two to U.S. servicemen killed in combat since the Sept. 11, 2001 attacks on the United States by al Qaeda Islamist militants.
The "9/11 generation of service members" understood that "people cannot live in freedom unless free people are prepared to die for it," he said.
Hollande declared that France "would never forget the solidarity between our two nations, solidarity based on a shared ideal, an aspiration, a passion for freedom."
Twenty-one foreign leaders attended the commemorations, including Britain's Queen Elizabeth and Prime Minister David Cameron, Canada's Stephen Harper as well as Merkel and Putin, whose country suffered the heaviest casualties and struck decisive blows on the eastern front to defeat the Nazis.