The Worthy Farm event reclaimed the title from 2010 winners Bestival at Tuesday evening's (November 15) ceremony, which was held at The Roundhouse in London.
However, Rob Da Bank's event received the 'Fan Favourite' award this year. The BBC Radio 1 DJ thanked festival-goers for their support on his Twitter account following the ceremony.
> Glastonbury 2011: In pictures
> Bestival 2011: The Cure, Katy B, PJ Harvey in pictures
Robert Richards, who is Glastonbury's director of sponsorship and marketing, told BBC 6Music: "Michael [Eavis] always tried to make the last festival before the fallow year a particularly special one.
"I think you can't take out of the equation the lineup we had, not just on the Pyramid Stage, which was phenomenal, but across the board I think we had some incredible acts play."
Glastonbury 2011 was headlined by Beyonce, Coldplay and U2.
Elsewhere, Sonisphere was given the 'Lineup of the Year' trophy and the Secret Garden Party claimed the prize for 'Best Medium-Sized Festival'.
End of the Road - which attracted acts including Mogwai, Wild Beasts and Joanna Newsom this year - triumphed in the 'Best Small Festival' category.
Awards for performances were given to Paolo Nutini, who was named 'Headline Performance of the Year' for his Latitude show, and Ed Sheeran, who took home the 'Best Breakthrough Artist' award.
Meanwhile, Derbyshire's Y-Not Festival - held each August in the Peak District National Park - was recognised with the 'Best Toilets' award, following in the footsteps of previous winners such as T in the Park and The Big Chill.
Watch Ed Sheeran performing 'You Need Me But I Don't Need You' at Latitude 2011 below: