Khamenei bestowed a kiss on Rohani's cheek and the new president kissed the leader on his lapel at the event, where Rohani spoke briefly to give his thanks and welcome the opportunity to serve the country.
The incoming president pledged to "take fundamental steps in elevating Iran's position based on national interest and lifting of the oppressive sanctions," according to AFP.
Rohani created a stir just 24 hours ahead of the confirmation ceremony with a swipe at Israel, withmisquotes by Iranian news agencies further complicating the situation.
Beyond the international isolation that eight years under hard-line President Mahmud Ahmadinejad have brought, Rohani is expected to face serious economic and social challenges at home.
The endorsement ceremony will be followed by a public inauguration in the parliament on August 4.
But under Iran’s constitution, Rohani’s four-year term of office begins when he receives the supreme leader's endorsement. Khamenei holds ultimate power in the political and religious areas under Iran's theocratic system. Four years after the brutally divisive reelection of Ahmadinejad, after which massive street protests broke out and the opposition claimed fraud, the supreme leader in his brief statement tried to stress the role of the ballot box in the June election that picked Rohani.
Rohani was scheduled to take his public oath of office in front of Iranian lawmakers and foreign dignitaries from 52 countries at the inauguration the next day.
Iran and the United States and its Western allies remain deadlocked over objections to Tehran's nuclear program, for which Iran has been criticized by the UN nuclear watchdog.