The tariffs are yet another chapter in a 16-year spat over subsidies for aircraft manufacturers Airbus and Boeing that turned increasingly sour under President Donald Trump.
French exporters were hit with hiked tariffs on wine and cognac, while Germany saw new levies on aeronautic parts.
"The Commission takes note of today's entry into force of US tariffs arising from the WTO Airbus case on aircraft subsidies," a statement said on Tuesday.
The EU executive handles trade matters for the bloc's 27 member states.
Looking forward to Biden
"As we have made clear before, we regret that the United States chose to add further EU products to its retaliation list," it said in a statement, adding that it was "looking forward to engage constructively with the new US administration to resolve this long lasting dispute as part of a renewed transatlantic agenda".
French wine and spirits exporters believe the new tariffs will cost the sector one billion euros in sales, with the cognac business especially punished.
FEVS, a French exporters' association, has estimated that the wine and spirit sector could lose more than 1 billion euros a year due to the tariffs unless incoming president Joe Biden reverses them.
In its last days in office, the Trump administration has appeared ambivalent on trade issues with the Europeans.
Washington last week suspended a plan to impose new tariffs on $1.3 billion in French products in a dispute over a digital services tax.
