Private Eye editor Ian Hislop described Nick Davies as "thoroughly deserving" of the accolade
Davies was announced as the winner at a ceremony held at the British Academy of Film and Television Arts headquarters in London.
The award was established by Private Eye and the Guardian in memory of campaigning journalist Paul Foot, who died in 2004.
It recognises the best investigative journalism, in this case based on work published in 2011.
This is one of a number of awards for Davies in relation to his investigations into phone hacking, with the award organisers having said that last year marked "the turning point with explosive revelations, the fallout from which continues across politics and the media".
In November Davies was named journalist of the year at the Foreign Press Association Media Awards 2011 and was also given the Frontline Club award in recognition of his phone-hacking investigation.
Commenting on Davies' win today, Private Eye editor Ian Hislop said in a release: "At a time when some commentators are suggesting that the entire press has lost its way, the shortlist for this award clearly demonstrates that the spirit of Foot's style of journalism is alive, well and kicking the people who matter.
"Nick Davies is a thoroughly deserving winner of this year's Paul Foot Award for an outstanding piece of work that has produced extraordinary results.
"This award is recognition of the cheering truth that the best journalism exposed the worst".
As the overall winner of the award Davies received a £5,000 prize. The runners up were named as Jonathan Calvert and Claire Newell for their 'Fifa World Cup scandal' series in the Sunday Times, with them both taking away a £1,000 prize.
The remaining finalists also received £1,000 prize money.
The winner for 2010 was freelance journalist and author Clare Sambrook for her reports on the detention of asylum seekers' children.