The two aviation giants have been locked for years in a sprawling set of disputes at the Geneva-based WTO.
Today's ruling concerns the so-called "baby Boeing" case, which relates only to tax breaks and other incentives provided by Washington State to the American aircraft maker.
Last November WTO judges found that one of the subsidies Washington State offered to support production of Boeing's 777X jet was "prohibited" as they encouraged the use of domestic materials, and thus caused trade distortions.
"The WTO has rejected yet another of the baseless claims the EU has made," Boeing said in a statement.
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According to Airbus's own estimates, Washington state has given Boeing tax breaks worth nearly nine billion dollars in a scheme scheduled to run through 2040.
Boeing has dismissed those numbers, putting the benefits to date at a maximum of USD 1 billion.
Brussels and Washington have two larger cases pending at the WTO, centred on multiple claims and counter-claims about illegal subsidies for their respective aviation industries.