The singer is said to have lip-synched her rendition of 'The Star-Spangled Banner' at the event, after she decided shortly before to use a studio-recorded version rather than sing live.
Keys - who also performed at the inauguration celebrations - described Beyoncé as an "incredible" artist who can "deliver" a great performance on any occasion.
"What I do know is that Beyoncé is a great performer and she's an incredible artist with a really, really powerful voice," she told Capital FM.
"The one thing that you cannot doubt is that she can sing. She absolutely can sing."
She added: "All the rest of the 'whys' or 'whatever', we know that she can deliver and she did deliver that song really beautifully."
Beyoncé has yet to respond to the claims that she mimed her performance on Monday.
Aretha Franklin - who performed the same song at Obama's 2009 inauguration - has said that she laughed when she first heard the claims.
She explained: "I thought it was funny because the weather down there was about 46 or 44 degrees and for most singers that is just not good singing weather.
"When I heard that I just really cracked up. I thought it was really funny, but she did a beautiful job with the pre-record."
Watch Beyoncé's performance of 'The Star-Spangled Banner' below: