Transitive Corporation, the only UK firm to make it through to the final stages of the competition, was recognised for the technological innovation of its QuickTransit software translator.
QuickTransit allows applications compiled for one processor or operating system to run on another without any reprogramming.
Founded in 2000, Transitive has headquarters in Los Gatos in California and a research and development team in Manchester in the UK.
The other two winners were Swedish company Telepo and Austrian firm Treventus Mechatronics.
Telepo won for a communications system that allows anytime, anywhere access to fixed-line phone services, while Treventus triumphed for its ScanRobot automatic scanner that digitises books in minutes.
Seven German companies reached the final, but the country failed to scoop a major prize.
A total of 450 companies in 30 European countries entered the competition, and 17 runners-up each received €5,000 ($8,367).
"Information and communications technology opens up a world of new possibilities, including new ways of working and new ways of living," said Information Society and Media Commissioner Viviane Reding, who awarded the prizes at the CeBIT show in Hanover.
"Innovations such as these are essential if Europe is to stay ahead in the global game."
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