Vahid Amiri scored the winner for Persepolis in the 37th minute at the Azadi Stadium.
Persepolis midfielder Mohsen Rabikhah was shown his second yellow card before the hour mark.
Sepahan is scheduled to face Sanat Naft on Saturday.
Persepolis moved top of the table with 34 points, three points above Sepahan.
Esteghlal is third with 29 points.