After his surprise election win in June, the 64-year-old seen as a moderate assumes Iran's highest elected office at a 1230 GMT ceremony presided over by Ayatollah Ali Khamenei.
Rowhani succeeds Mahmoud Ahmadinejad, whose turbulent double-term presidency was marked by frequent outbursts against the Jewish state and a disputed re-election that saw a heavy-handed crackdown on dissent.
Ahmadinejad's eight years in office were also marked by showdowns with Western powers over Tehran's nuclear ambitions and economic suffering because of international sanctions and mismanagement.
Rowhani's remarks about Israel on Friday showed that Iran's new president will also be no stranger to controversy on the international stage.
During annual rallies on Quds (Jerusalem) Day, he labelled Israel a "wound" on the Muslim world, sparking a sharp response from Israeli Prime Minister Benjamin Netanyahu.
"In our region, a wound has for many years been sitting on the body of the Islamic world in the shadow of occupation of the holy land of Palestine and the dear Quds," Rowhani said in remarks broadcast on state television.
But his comments were originally misquoted by official media that reported him as saying "the Zionist regime is a wound inflicted for years on the body of the Muslim world that must be cleansed".
Netanyahu swiftly denounced Iran's president-elect, based on his remarks as initially reported.
"Even if the Iranians work to deny these comments, this is what the man thinks and reflects the regime's plans," he said.
Rowhani on Friday also pledged allegiance to the Palestinian cause and rejection of Israel as a state, an unfaltering cornerstone of Iranian foreign policy since the 1979 Islamic revolution toppled the US-backed shah.
However, during campaigning and also after his election, Rowhani also vowed to engage constructively with the international community.
The former nuclear negotiator also said there would be increased transparency in Iran's atomic activities which the West suspects have a military motive, despite repeated denials.
After his endorsement by the supreme leader on Saturday, on Sunday Rowhani will take the oath of office in a swearing-in ceremony in parliament.
He will then officially have two weeks to name his cabinet and the conservative-dominated parliament will have 10 days to review the list and vote on the nominees.
Multiple lists of nominees have appeared, with many of those mentioned having been educated in the United States and Britain.
Rowhani himself earned a doctorate in constitutional law in Scotland.
Media reports say Sunday's swearing-in will be attended by 10 regional presidents and other high-ranking officials.
One notable guest will be Javier Solana, the former European Union foreign policy chief who has represented world powers in nuclear talks with Tehran.
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