The account had a short notice reading "X suspends accounts which violate the X Rules," though the Elon Musk-owned platform did not specify which rule had been violated.
Khamenei's office runs several social network accounts in his name, broadcasting messages in different languages.
The Hebrew-language account had launched on the weekend with a message that is a common greeting in the Islamic world: "In the name of Allah, the Benevolent, the Most Merciful."
It was opened after Israel carried out air strikes against military sites in Iran on Saturday in response to Tehran's missile attack on October 1.
At least four Iranian soldiers were killed in the attack which Iran said caused "limited damage" to a few radar systems.
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