Accepting the award, Guardian editor Alan Rusbridger said there was a need to "think carefully" about WikiLeaks founder Julian Assange and alleged source Bradley Manning.
"I think it's too early to say what effect that story had on the events in the Middle East and North Africa, but I would guess it had some effect.
"And the reason we went to the New York Times with that story to share it with them, was mainly because of the First Amendment which is the gold standard of free speech in the world.
"At a time when our own libel laws are being reformed I just think we ought to think carefully and hope the Obama Administration will think about what it does about Julian Assange and Bradley Manning. We've had our ups and downs with him [Assange], he's an interesting man, a brilliant man and a difficult man, but I think the eyes of the world are on how America will react."
The Guardian took away four awards on the night, with reporter Andrew Sparrow named Political Journalist of the Year, Amelia Gentleman winning Feature Writer of the Year and its World Cup 2010 guide named Special Supplement of the Year.
The News of the World also won four awards, with Stephen Moyes named Showbiz Reporter of the Year, Mazher Mahmood named News Reporter of the Year, its Fabulous magazine named Supplement of the Year and its cricket corruption story named Scoop of the Year.
In order to preserve his anonymity, Mahmood was not on hand to collect his award, which was accepted by News of the World editor Colin Myler instead.
Times columnist Caitlin Moran took away two awards for Critic of the Year and Interviewer of the Year, two out of five a total of five awards for the Times.
The London Evening Standard won two awards for its Dispossessed Campaign, both the Campaign of the Year Award and the Cudlipp Award, which recognises excellence in popular journalism.
The full list of winners:
Young Journalist of the Year: Matt Sandy, The Mail on Sunday
Business and Finance Journalist of the Year: David Robertson, The Times
Political Journalist of the Year: Andrew Sparrow, The Guardian
Foreign Reporter of the Year: Charles Clover, The Financial Times
Showbiz Reporter of the Year: Stephen Moyes, News of the World
Specialist Journalist of the Year: Brian Deer, The Sunday Times
Critic of the Year: Caitlin Moran, The Times
Photographer of the Year: Matt Cardy, Getty Images
Sports Photographer of the Year: Mark Pain, The Mail on Sunday
Sports Journalist of the Year: James Lawton, The Independent
Feature Writer of the Year: Amelia Gentleman, The Guardian
Interviewer of the Year: Caitlin Moran, The Times
Columnist of the Year: Matthew Parris, The Times
News Reporter of the Year: Mazher Mahmood, News of the World
Cartoonist of the Year: Peter Brookes, The Times
Regular Supplement of the Year: Fabulous, News of the World
Special Supplement of the Year: World Cup 2010 Guide, The Guardian
Front Page of the Year: Pinickio, The Daily Mirror
Scoop of the Year: Cricket Corruption, News of the World
International Journalist of the Year: Ibrahim Essa
Campaign of the Year: The Dispossessed, London Evening Standard
Digital Innovation of the Year: Mail Online, Daily Mail/Mail on Sunday
The Cudlipp Award: London Evening Standard, The Dispossessed campaign
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