Khamenei, 85, has served as supreme leader of the Islamic Republic since 1989, when he succeeded Ayatollah Ruhollah Khomeini, the leader of the 1979 Islamic Revolution.
The prosecutor noted that all of Iran’s military and foreign policies are carried out at his behest.
Eighty-five people were killed and more than 300 were wounded in the July 18, 1994 bombing at the AMIA (Asociación Mutual Israelita Argentina) Jewish community centre, the deadliest terrorist attack in the country’s history.
Last year, an Argentine court said that Iran was responsible for the attack, using its Lebanese terrorist proxy Hezbollah.
Ali Khamenei has previously denied the allegations.