Saei received eight of 15 votes to secure the position.
Archer Zahra Nemati – a two-time Paralympic champion – finished second in the voting.
Fencer Mojtaba Abedini was elected vice-chairman, edging out table tennis’ Afshin Norouzi.
Judoka Arash Miresmaeili, twice a world champion, previously chaired the Athletes’ Commission.
Saei is Iran’s most decorated Olympian.
He won Olympic gold in the men’s 68-kilogram division at Athens 2004 and added a second title in the 80kg class at Beijing 2008, having won a bronze medal at Sydney 2000.
Saei is one of only two Iranians to have won a pair of Olympic gold medals, alongside weightlifter Hossein Rezazadeh.
Earlier this year, 44-year-old Saei was been appointed technical director of the Islamic Republic of Iran Taekwondo Federation.
By: Inside the Games