Paul Lewis was also shortlisted for the Orwell Prize earlier this year for his riots coverage on Twitter
The site "gets the right balance between serious news and lighter features and sports and it is so easy to navigate", according to a release.
"Online, it still looks and feels and walks and talks like a newspaper and the online site is just as attractive as the print edition."
Guardian special projects editor Paul Lewis took the award for best Twitter feed. His tweets reporting on the England riots were among the nominations which led to Lewis being shortlisted for the Orwell Prize reporter of the year award earlier this year.
Another of the Guardian's five awards was for its use of social media during the riots. The title also received an accolade for its iPad edition.
The chairman’s award went to the Mail Online "to recognise its success in terms of increasing its monthly users and global reach". Yesterday ABC-audited web figures show the Mail Online had 91,687,074 monthly visitors in May.
The Sunday Times, The Times and the BBC each won two awards.
The Sunday Times took the prize for best campaigning or investigative journalism and for best photography, The Times won the in the citizen journalism category for its cities fit for cycling campaign and the BBC was named best site for news-led journalism and best for video journalism.
The Fact Check blog from Channel 4 News won the award for blogging prize, Red Online won best designed site, The Arts Desk along with The Economist won best specialist site for journalism, and the Belfast Telegraph took the award for the best local or regional news site. The Student Nursing Times won the award for best brand development.
Carla Buzasi, editor-in-chief and the Huffington Post UK, was named online editor of the year for "successfully launching into the UK and bringing the bold direct magazine presentation to the news site and making a big splash in a competitive market".
The awards were sponsored by IE School of Communication, the Press Association, Society of Editors, NUJ and Holdthefrontpage.co.uk.