Giorgi Gvelesiani found the back of the net from the penalty spot just four minutes into the match and Vahid Amiri made it 2-0 five minutes later.
Havadar pulled a goal back from the penalty spot in the 61st minute but Issa Alekasir scored Persepolis’ third goal in the 72nd minute.
Persepolis will play Esteghlal in the final match, scheduled for May 31 in Tehran’s Azadi Stadium.
Esteghal is the most successful club with seven titles, followed by Persepolis which has won six times.