Ezatollah Pourghaz gave the lead the host with a long-range shot in the 73rd minute.
Soon after, Persepolis put Sepahan under pressure but the team’s strikers failed to score.
Referee Alireza Faghani showed the penalty in the 89th minute after the ball was touched by Sepahan defender.
Ali Alipour found the back of the net from the spot.
Sepahan striker Kiros Stanley was sent off in the injury time after receiving his second yellow card and Kamal Kamyabinia was also shown a straight red card.
Sepahan moves top of the IPL with 30 points thanks to a superior goal difference over Padideh.
Persepolis remains third with 28 points.