Click here to see the full list of winners
Mike Smartt, BBC News Online's editor-in-chief, said he was delighted at the site's People's Voice Webby.
He said: "To be voted best by web users in such a remarkable year for news, on top of last year's judge's award, is doubly pleasing because they are the fiercest critics.
"It reflects outstanding work by the great team at BBC News Online."
The Webbys are given out in 31 categories by The International Academy of Digital Arts and Sciences.
The categories cover topics as diverse as news, games, humour and spirituality.
They reward net innovation, hard work and the best that the web has to offer.
Winners this year came from a record 24 different countries.
Nasa won two awards winning in both the education and government categories.
Humour was won by Get Your War On, and the "weird" category was topped by British site Rathergood.