The Reds defeated the home side 2-1 at the newly-established 15,000-seater Shahid Mofatteh Stadium in the city of Hamedan on Thursday evening.
The hosts took the lead when Hadi Asghari scored the opener five minutes after the break.
Persepolis substitute Mohammad Parvin, however, leveled maters in the 74th minute with a fantastic free kick and Hadi Norouzi netted the winner two minutes from time.
The Persepolis, coached by Croatia's Zlatko Kranjcar, drew its first two matches of the season against Mes Kerman and Esteqlal-e-Ahvaz.
The win has moved Persepolis to the second place of the IPL table with five points. Esteel Azin currently tops the standings with six points after three weeks.