Germany designated Hezbollah a "Shia terrorist organisation" on Thursday as its security forces raided mosques and associations linked to the group.
Iran argued Germany was motivated by the grim legacy of Nazi rule and its guilt over the Holocaust, the mass murder of six million European Jews in labour and extermination camps.
"We feel the Germans seems to have a historical debt to the Zionists and are repaying it somehow, and don't realise that the world and Muslims might react," said foreign ministry spokesman Abbas Mousavi.
Hezbollah was established in 1982 during the Lebanese civil war and fought a 2006 war with Israel.
The United States and Israel have long designated it a terrorist group and urged allies to follow suit.
Like the European Union, Germany had until now outlawed only Hezbollah's military wing while tolerating its political arm, a major force in the Lebanese parliament.
Iran's Mousavi criticised Germany's mosque raids and charged that "it is not appropriate to attack all Muslims if they feel a group of them are doing something illegal, which we don't see as such".
Tehran is a major supporter of the Lebanese group and its "resistance" against the Islamic republic's arch foe Israel.
Iran's state-owned and ultra-conservative Kayhan newspaper had on Saturday similarly attacked Germany in an article that also denied the Holocaust.
"Branding Hezbollah as a terrorist group is an order dictated to you by Israel, not a decision you made independently!" wrote Kayhan's managing director and editor-in-chief Hossein Shariatmadari.
Shariatmadari was personally appointed by Iran's supreme leader Ayatollah Ali Khamenei in 1993.
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