The Tehran giants finally unveiled their new boss after speculation linking them with former Senegal boss Bruno Metsu and ex-Argentina international Gabriel Calderon
The 66-year-old Portuguese, who last worked with Egyptian club Al Ahly, has agreed a one-year deal with the Tehran giants.
Manuel Jose is regarded as a legend in Egypt following much success with Al Ahly including six league titles and a third place finish at the 2006 Fifa Club World Cup, but left the club in the wake of the Port Said tragedy earlier this year.
The Portuguese has previously worked in West Asia with Saudi Arabian outfit Al Ittihad, however he last little more than six months with the club.
Manuel Jose replaces Turkish boss Mustafa Denizli who quit Persepolis last month due to personal reasons. Bruno Metsu and Gabriel Calderon had also been linked with the position.
The nine-time Iranian champions endured a difficult 2011-12 campaign, finishing down in 12th spot and bowing out of the AFC Champions League at the Round of 16.