Iran and Hezbollah are both sworn enemies of Israel and the Lebanese Shiite group has received Tehran's moral, financial and military support since its inception.
Iran "strongly denounces the (EU) decision... And believes (it) is in line with the illegitimate interests of the Zionist regime," Foreign Minister Ali Akbar Salehi was quoted as saying by official media.
"The European Union, due to lack of correct judgement about the regional crisis, took this wrong decision," Salehi said.
Hezbollah fought a bitter war with Israel in 2006 and more recently has been providing military support to the regime of Syrian President Bashar al-Assad as it tries to put down an insurgency that has escalated into civil war.
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Salehi's comments come after the EU yesterday put Hezbollah's military wing on its of terrorist organisations, a move the Lebanese Shiite movement slammed as aggressive and unjust.
To get the required agreement of all 28 EU member states, ministers had to overcome reservations in some members that the move would further destabilise Lebanon, where the militant group plays a key role in politics and has dominated the government since 2011.
Hezbollah's military wing was blamed for a deadly attack on Israeli tourists in Bulgaria last year.
In March, a Hezbollah operative was also convicted in Cyprus of plotting a similar attack.
Iran and Hezbollah have remained steadfast allies of Assad's regime throughout the conflict roiling Syria.