The project saw the MEN analyse tweets from Greater Manchester Police, which was tweeting every reported incident over a 24-hour period on the 14 October last year, breaking down and visualising the incidents as close to real time as possible.
The judges praised the project for breaking new ground in live data journalism.
MEN head of online content Paul Gallagher told Journalism.co.uk today that he was "really pleased" with the award, "mainly because there were so many people involved in the project".
"We were analysing more than 3,000 tweets on the day and we had about 10 journalists involved who each analysed some of the data. Because it was such a big lump of data we had to get almost the whole newsroom involved.
"And one of the developers from the website got involved too."
Gallagher said his team would pursue more data projects in the future and learn from the lessons of the GMP 24 project.
"Obviously the GMP thing came before the Police.uk data was available. Now we have access to that data and we are looking to use it to provide a more detailed pictured of crime in our communities."
The Irish News was the biggest winner at this year's awards, taking home three prizes including Regional Newspaper of the Year.
The title was also named Best Daily/Sunday Newspaper with a circulation above 25,000 and reporter Alison Morris won Daily/Sunday reporter of the Year.
Judges decribed the title as "a serious newspaper that was prepared to take a stance; a heavyweight title at the heart of one of the newsiest cities in the world".
The Irish News was also highly commended in the Campaign of the Year category, which was won by the Norwich Evening News for its End the Indignity campaign, which targeted NHS management of care provision.
The Kent Messenger's political editor Paul Francis won Weekly Reporter of the Year.
Paul Gallagher will be speaking about the MEN's digital innovation at Journalism.co.uk's upcoming news:rewired conference. See the full agenda at this link.