The 28 ministers condemned the military offensive that the Syrian government is waging against rebels and called for an immediate ceasefire to allow humanitarian access.
US, French and British missiles destroyed suspected chemical weapons development and storage sites in Syria on Saturday in response to an alleged chemical attack in the town of Douma.
In a statement after talks in Luxembourg, EU foreign ministers unequivocally blamed President Bashar al-Assad's regime for the Douma attack and gave implicit backing to Saturday's Western military action.
"The Council understands that the targeted US, French and UK airstrikes on chemical weapons facilities in Syria were specific measures... with the sole objective to prevent further use of chemical weapons and chemical substances as weapons by the Syrian regime to kill its own people," the statement said.
"The Council is supportive of all efforts aimed at the prevention of the use of chemical weapons."
French Foreign Minister Jean-Yves Le Drian said the EU was "united at a very serious moment" in wanting to "prevent and dissuade against any use of chemical weapons."
British Prime Minister Theresa May and French President Emmanuel Macron on Monday faced anger from lawmakers for conducting air strikes with the US in Syria.
May was due to address MPs after proceeding with the joint strikes without prior parliamentary approval - a sensitive subject in Britain where memories of participation in the US-led invasion of Iraq in 2003 are still raw.
Jeremy Corbyn, leader of the main opposition Labour Party, has said the strikes were "legally questionable" and called for new legislation to stop governments launching military action without lawmakers' backing in most circumstances.
"I believe that parliament should have been consulted and voted on the matter. The UK prime minister is accountable to parliament, not to the whims of a US president," he wrote in a weekend letter to May.
Stop the War Coalition called for a demonstration on London's Parliament Square at 5:30 Monday.
The group said the strikes "will have done nothing to end the war" and "risked dramatically widening" the conflict.
The leaders of the opposition Scottish National Party and Liberal Democrats have also criticized May and there is the possibility of a vote in parliament later Monday that could embarrass the prime minister if she loses.
In France, Macron has faced similar criticism for attacking Syria without consulting the legislature but defended the move as well as his constitutional powers in a TV interview on Sunday.
"This mandate is given democratically to the president by the people in the presidential election," he said.
Macron also said he had convinced US President Donald Trump to stay engaged in Syria "for the long-term."
Macron has been criticized from both right and left.