The Reds beat Foulad Gostar 3-1 in the second leg to win 4-1 on aggregate.
Persepolis ended the first half 2-0 through Tiago Alves and Hamid Ali Asgar.
Rasoul Khatibi narrowed the lead in the 73rd minute, four minutes before Mohsen Khalili sent cheers to thousands of Persepolis fans at Tehran's Azadi Stadium.
Sepahan, Zob Ahan and Esteqlal have already secured the three top spots in Iran's Premier League to play in next year's AFC-CL.