Mr Raisi and Foreign Minister Hossein Amir-Abdollahian were murdered in a helicopter crash in the mountains of northwestern Iran.
According to state media, they were killed when the helicopter they were flying in crashed on Sunday.
Ayatollah Khamenei expressed his condolences “to the dear people of Iran”.
Mr Raisi, 63, was seen as a potential successor to the supreme leader.
Following the president’s death, Vice President Mohammad Mokhber has been selected to serve as interim president.
Mr. Mokhber will work with the presidents of Iran’s legislative and judiciary to prepare for a presidential election within 50 days.
