More than 1,700 people were killed in attacks mostly targeting the Alawite community, which is associated with the clan of ousted ruler Bashar al-Assad, in Syria's coastal region in March.
The groups targeted “civilians and especially the Alawite community, including by committing arbitrary killings”, the EU's official journal read.
The latter was held responsible for “serious human rights abuses in Syria, including torture and arbitrary killings of civilians”.
US President Donald Trump has also announced the lifting of sanctions on Syria, ending more than a decade of diplomatic freeze.
But EU diplomats had warned the 27-nation bloc intended to impose new individual sanctions on those responsible for stirring ethnic tensions.
Syria's 14-year civil war killed more than half a million people and ravaged the country.
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