A German court awarded victory in the case to businessman Daniel Giersch, who runs the Gmail.de website.
Giersch has owned his trademark since 2001 and has been in dispute with Google over its email service since 2004.
However, Google downplayed the legal ruling, maintaining that it would not affect its email services.
"The decision of the Office for Harmonisation in the Internal Market not to have the Gmail trademark registered on a pan-European basis will have no effect on the current use of the Gmail trademark in Europe," said a Google spokeswoman.
"Outside Germany and the UK, where Google's web mail service is called 'Google Mail', the product will remain with Google's trademark 'Gmail'."
The spokeswoman insisted that there would be no changes in the Gmail experience for users in Europe, and no changes for Google Mail users in Germany and the UK.
Giersch had already won both the preliminary and final stages of the case in a 2006 ruling from a district court in Hamburg, forcing Google to remove all Gmail references from its German service.
Google had previously lost the rights to the name in the UK, following a 2005 out-of-court settlement with financial research company IIIR.
Giersch claimed that Google offered him $250,000 (£127,000) to drop the case, and said that he found the company's actions "very threatening, very aggressive and very unfaithful".
He is currently defending similar claims in Monaco, Switzerland and Norway.
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