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It's the latest twist in a long-running dispute over support provided by European and US governments for the world's biggest airplane manufacturers.
Wednesday's ruling, which will affect less than 2% of the value of total EU exports to the United States, could further inflame trade tensions with the Trump administration.
If the United States goes ahead with the tariffs, as seems likely, Europe will retaliate.
The top EU trade official said that the bloc had shared proposals with the United States as recently as July for "a new regime on aircraft subsidies" but had so far received no response.
"Our readiness to find a fair settlement remains unchanged," EU Trade Commissioner Cecilia Malmström said in a statement. "But if the US decides to impose ... countermeasures, it will be pushing the EU into a situation where we will have no other option than do the same."
In the coming months, the WTO will determine the amount of countermeasures the European Union can impose on US products because of unfair subsides to Boeing.
If both sides elect to impose tariffs, this "would only inflict damage on businesses and citizens on both sides of the Atlantic, and harm global trade and the broader aviation industry at a sensitive time," Malmström added.
Airbus reiterated calls for talks, saying tariffs would be a "barrier against free trade" and negatively affect airlines, travelers and jobs in the United States.
"Airbus is therefore hopeful that the US and the EU will agree to find a negotiated solution before creating serious damage to the aviation industry as well as to trade relations and the global economy," CEO Guillaume Faury said in a statement.
Transatlantic trade is already facing increased friction. The US has imposed tariffs on European steel and aluminum exports.
The EU retaliated with tariffs on more than $3 billion worth of American exports in June. The levies hit products such as motorcycles, orange juice, bourbon, peanut butter, cigarettes and denim.
The trading relationship is worth more than $1 trillion annually, but Europe exports significantly more goods to the United States than the other way around.
In 2018, the European Union exported €407 billion ($445 billion) worth of goods to the United States. US exports to the European Union totaled $318 billion. And the July goods deficit with the European Union — at $20.1 billion — was the highest on record, according to the US Census Bureau.
The WTO on Tuesday slashed its forecast for world trade growth in 2019 to 1.2% from 2.6%.