Israeli Prime Minister Benjamin Netanyahu had said there were many signs Mr Khamenei had been killed in the strikes targeted against his residence.
The death of Mr Khamenei, 86, ends his reign of over three decades over Iran.
The Israeli prime minister said Israel, in collaboration with the U.S., coordinated the bombing of Iran on Saturday.
Nearly two weeks ago, Mr Trump had indirectly threatened Khamenei, saying he was an easy target.
Iran’s Supreme Leader Ali Khamenei said his country and Syria should expand their cooperation to overcome political and economic pressure from the U.S. and Europe.
