The drummer took to the stage with Sheeran, Mike Rutherford from Genesis and Richard Jones of The Feeling to play 'Wish You Were Here' on Sunday (August 12).
However, Sheeran came under fire from Pink Floyd fans for his rendition of the track, particularly after his younger fans mistook the song for Sheeran's new single.
"Following a bit of post-show stuff with some of the PF fans getting outraged at people not realising the song was not your new release, I just wanted to go on record to suggest they chill on this," Mason wrote in an email later tweeted by Sheeran.
"As far as I'm concerned, what you did was a really great version of the song.
"It's one of the nicest tributes to have any artist choose to play another's work, particularly an artist who's a great songwriter in his own right.
"Sooner or later people will work out the origin of the song and, who knows, maybe check out our catalogue, just as, hopefully, our fans might check out yours.
"Music doesn't have to be entirely partisan - or if it does, no-one bothered to tell me."
Photo gallery: London 2012 closing ceremony:
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