The Blues mostly dominated the game but had to wait 41 minutes before Brazilian midfielder Fabio Janvario could score the winner on Sunday in Mashhad.
Esteqlal also missed a chance to double the lead when the IPL's top scorer, Arash Borhani, failed to convert a penalty in the 85th minute.
The Blue partly owe their second championship to Zob Ahan who conceded a humiliating 4-1 defeat to Foulad Khuzestan in Ahwaz only to see its first chance to win the championship gone with the wind.
The last time that the Blues had lifted a trophy dates back to the 2005-06 season when Esteqlal was named IPL champion again under Amir Qalenoi.
Earlier in the day the Blue's arch rival, Persepolis, managed to defeat Rah Ahan 2-0 in a vague attempt to make up for an embarrassing 5-1 defeat against Qatar's Al Gharafa in the AFC champions League.