The EU's Official Journal -- the bloc's record of decisions and their implementation -- added the "Hezbollah Military Wing" to the list of 11 persons and 25 groups deemed to be involved in terrorist activity.
The listing will most likely result in an assets freeze but analysts have warned it may be virtually impossible in practice to distinguish between Hezbollah's military and political wings.
Others on the list include Hamas, the Palestinian militant group that rules Gaza, Colombian rebel group FARC, Peru's Shining Path and the Communist Party of the Philippines and its armed wing.
To meet these concerns, ministers agreed that the blacklisting of Hezbollah would not "affect legitimate financial transfers to Lebanon and the delivery of assistance, including humanitarian assistance," the Official Journal said.
Also Read
The Lebanese government last week had called on the EU not to list Hezbollah which it said played a key role in the country.
Hezbollah describes itself as a resistance movement against Israel, which occupied south Lebanon until 2000. It plays a dominant role in Lebanese politics and is part of the government.
Hezbollah chief Hassan Nasrallah said on Wednesday that the decision means the EU will share responsibility for any future Israeli attack on Lebanon.