Cobain took the accolade and a cheque for £5,000 for his investigation into Britain's involvement in the torture of terror suspects detained overseas.
Journalism.co.uk spoke to the prize winner following the announcement for his thoughts on investigative journalism [More to follow].
The senior reporter beat a shortlist nominating eight journalists - six individuals and two partnerships - including the Telegraph's Ben Leapman for the MPs' expenses investigation and the Yorkshire Post's Rob Waugh.
The shortlist in full was:
Jonathan Calvert and Clare Newell, Sunday Times (financial and legislative abuses in the House of Lords)
Ian Cobain, The Guardian
Ben Leapman, Sunday and Daily Telegraph (MPs' expenses investigation)
Paul Lewis, The Guardian (investigation into the death of Ian Tomlinson at the G20 protests)
Rob
Waugh, Yorkshire Post (investigation into 'cavalier' spending at Leeds
Metropolitan University; investigation into Leeds City Credit Union)
Stephen Wright and Richard Pendlebury, Daily Mail (investigation into lawyer Shahrokh Mireskandari)
The Private Eye and Guardian prize is given in memory of Paul
Foot, the campaigning journalist who died in 2004.