Persepolis was formerly beaten by Paykan 2-1 in the first leg in Tehran’s Azadi Stadium.
An early own goal from Hossein Memar put Persepolis in the lead nine minutes into the match.
Persepolis captain Karim Bagheri hit the second goal before the halftime. His shot was deflected by Paykan’s defender and went to the far post.
Paykan pulled a goal back when Persepolis keeper Alireza Haghighi failed to save a long range shot from Jahangir Asgari in the 61st minute.
Persepolis striker Mohsen Khalili rubbed salt into Paykan’s wounds opening the goal with a good flick in the 75th minute.
“I am so happy to win an away game after months. Persepolis showed a good performance against Paykan and we gained three vital points. Persepolis will beat Esteghlal in the Tehran derby next week,” Persepolis coach Ali Daei said in a post-match news conference.
Persepolis is fourth in IPL standings table with 40 points. Sepahan remains on the summit of the table with 49 points and one game fewer. Zob Ahan is second with 45 points.