President Barack Obama praised Joe Biden for his “faith in your fellow Americans, for your love of country and your lifetime of service”.
The award comes as both men prepare to leave office when Donald Trump is inaugurated on January 20.
The vice-president has said he plans to stay active in Democratic Party politics.
A visibly emotional Joe Biden stood by as President Obama heaped praise on what he called the “best possible choice, not just for me, but for the American people”.
According to the New York Times, the medal was awarded with distinction.
That additional honor has been reserved in recent administrations for just a handful of recipients, including Pope John Paul II.
Barack Obama joked that the internet would have one last chance to mock the pair’s “bromance”.
Joe Biden said he was “part of the journey of a remarkable man who did remarkable things”.
The vice-president said that he had had no idea the award was coming.
“I had no inkling. I thought we were coming over to Michelle for you, Jill and Barack and I and a couple of senior staff to toast one another and say what an incredible journey it’s been.
“Mr. President, you got right the part about my leaning on Jill but I’ve also leaned on you and a lot of people in this room.
“Mr. President, I’m indebted to you. I’m indebted to your friendship. I’m indebted to your family.”
Barack Obama said that Joe Biden’s career was “nowhere close to finished” both at home or abroad.
The vice-president has said he plans to work on policy issues at institutes at the University of Delaware and University of Pennsylvania, and continue his efforts tackling cancer, which claimed his son Beau in 2015.
Joe Biden gave an hour-long interview with media outlets on January 12 in which he strongly criticized Donald Trump for his condemnation of the US intelligence services.
“It is really very damaging in my view to our standing in the world for a president to take one of the crown jewels of our national defense and denigrate it,” he said.
“It plays into, particularly now, the Russian narrative that America doesn’t know what it’s doing.”
However, Joe Biden was full of praise for his successor, Mike Pence, saying he had sent him memos on how to handle certain situations.
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