He honoured 21 people with the Presidential Medal of Freedom in the White House, including actors Tom Hanks, Robert De Niro, Robert Redford and Cicely Tyson, and musicians Bruce Springsteen and Diana Ross.
Philanthropists Bill and Melinda Gates and basketball players Michael Jordan and Kareem Abdul-Jabbar were also among those honoured.
The president said of DeGeneres that said she has a way of making people laugh at something rather than someone “except when I danced on her show”.
He said it is also easy to forget that she had risked her career nearly 20 years ago when she came out as gay.
“What an incredible burden that was to bear, to risk her career like that. People don't do that very often, and then to have the hopes of millions on your shoulders,” Mr Obama said.
The Presidential Medal of Freedom recognises especially meritorious contributions to the national interests of the US, its security and its culture.
Mr Obama called the 2016 group a “particularly impressive class” and said they had inspired him over the years and “helped make me who I am”.
“Everybody on this stage has touched me in a very powerful, personal way, in ways that they probably couldn't imagine,” Mr Obama said in concluding an hour-long ceremony in the White House East Room.
Of “The Boss,” he said Springsteen crafted “anthems of our America, the reality of who we are and the reverie of who we want to be”.
Others receiving the award included Frank Gehry, one of the world's leading architects, Maya Lin, the designer of the Vietnam Veterans Memorial and Lorne Michaels, producer of the TV comedy show Saturday Night Live.
The diverse group seemed to enjoy themselves at the White House, participating in a mannequin challenge before the ceremony, trying not to move as they were recorded on video.
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