The appointment led to widespread criticism, even within pro-Ahmadinejad circles, because of an earlier remark by the vice president that Iran's political differences with Israel had nothing to do with Israelis and Jews and that Iran was a friend of the Israeli people.
While Ahmadinejad needs parliamentary approval for his ministers, he is free to select his vice presidents.
According to the constitution, however, the supreme leader has the final say on all state affairs and can veto executive and legislative decisions.
This is the second time in five weeks that Khamenei, who had put his stamp of approval on Ahmadinejad's re-election, openly voiced criticism of the president.
The first time was at the Friday prayer ceremony June 19 when he blamed Ahmadinejad for having accused ex-president Akbar Hashemi-Rafsanjani of corruption without presenting any documents proving the accusations.