The 'Born This Way' singer scooped the prize, which was voted for by over 1.5 million members of the public.
GaGa also picked up awards in four other categories; for 'Best Track', 'Best Female', 'Best Video' and 'Hottest Female', fending off competition from Cheryl Cole and Rihanna.
Virgin Media editor-in-chief of digital entertainment Nick Forward said: "The shock result for me was Lady GaGa beating Adele to win 'Best Album'. Adele's 21 has spent a record breaking 18 consecutive weeks at number one, so for Lady GaGa to swoop in and win this award was a huge surprise.
"It just demonstrates the incredible power of her fanbase. The results are never quite as we predict but at the end of the day, with over 1.5 million voters, these results really do reflect the voice of the public."
Other surprise wins included Cliff Richard, who picked up 'Legend of the Year' over Amy Winehouse and Tony Bennett. However, the pair's recent duet 'Body and Soul' beat Maroon 5 and Christina Aguilera's 'Moves Like Jagger' for 'Best Collaboration'.
Adele recently picked up six Grammy awards for 21, including 'Album of the Year' and 'Song of the Year'.
> Lady GaGa: 'Adele deserved every Grammy she won'
Watch Lady GaGa's 'Marry The Night' music video below: