It was the third successive year that Channel 4 News has won the Amnesty award, and the second year that the programme's reporting on Sri Lanka has scooped the top prize.
The Channel 4 News entry comprised reports from last year that showed further film purporting to show the execution of Tamil soldiers - and forensic investigation that led to some of the victims being identified.
Some of the reports were aired as President Rajapaksa visited the UK late last year - and were though to be behind his visit being cut short. The films have been cited in a recent investigation by the UN and will feature as part of a Channel 4 documentary later this month.
Commenting on the award, Jim Gray Editor of Channel 4 News said: "Huge congratulations to Ben De Pear and his team for cracking journalism and sheer dogged persistence on this story.
"Our achievements on Sri Lanka are genuinely important and, as ever, it was the result of a great team effort, so thank you to Jonathan Miller, Nevine Mabro, Sarah Corp and Girish Juneja - the editors that worked on very difficult footage - and of course those who must remain unnamed."
The judges comments were:
"The piece was streets ahead and it should not preclude it winning because it's the second year in a row. It should be rewarded for depth, effort and staying with the story.
"Keeping a story going is more challenging than finding new ones, in many ways.
"I was impressed by the commitment from the team, and the impact of their work is still to come: it could result in a UN inquiry. There is a chance of real tangible impact.
"Disturbing, deep, important."
Another Channel 4 News nomination shortlisted in the TV News category was Lindsey Hilsum's film on the women raped in the Congo - a powerful piece which was also part of Lindsey's winning portfolio as One World Journalist of the Year.
The Channel 4 News Online team were also shortlisted in the Digital Media category for an entry comprising special reports on the use of US drones in Pakistan.
The Amnesty Media Awards recognise excellence in human rights reporting and acknowledge journalism's significant contribution to the public awareness of human rights issues. You can see a full list of award winners here.
- Sri Lanka footage: behind the UN verdict 02 February 2010
- Sri Lanka 'war crimes' video: woman's body identified 08 December 2010
- Sri Lanka: civil war 06 April 2011