Omid Noorafkan found the back of the net for Sepahan with a long-range shoot in the 50th minute.
Arsalan Motahari leveled the score eight minutes later.
Ramin Rezaeian scored Sepahan’s winner in the added time from the penalty spot.
Sepahan moved up to second place with 30 points, two points behind Persepolis.
Furthermore, Malavan edged past Paykan 1-0 and Mes Rafsanjan drew 1-1 with Nassaji.