The Blues edged past their visitors from the central province of Shiraz after Captain Farhad Majidi scored a winner in the stoppage time at Tehran's Azadi Stadium on Friday afternoon.
The Blues took the lead when midfielder Kianoush Rahmati opened the scoring with a perfectly executed free kick, 22 minutes into the game.
Esteqlal's 32-year-old skipper managed to double the advantage upon intercepting Arash Borhani's pass just before half-time.
Mehrdad Karimian reduced the deficit in the 47th minute striking the net at a moment when Esteqlal goalkeeper Mohammad Mohammadi had strayed out of the penalty area.
Esteqlal defender, Amir Hossein Sadeqi scored an own goal in the 90th minute of the game, but Majidi netted the winning goal two minutes later to help his side move into third place in the Iranian Premier League (IPL).
Sepahan now leads the IPL table with 40 points after 19 games. Zob Ahan stands second with 36 points, followed by Esteqlal with 30.
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