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)
Free daily newsletter
- Russian newspaper editor-in-chief Dmitry Muratov receives Golden Pen of Freedom award
- Announcing the next editorial events from Journalism.co.uk
- BBC, Vice and Al Jazeera win big at Online Media Awards
- Announcing the next news:rewired digital journalism conference
- Announcing the agenda for the next news:rewired