In the match held at Azadi Stadium, Joséin Kana Anizadegan led Persepolis from a penalty spot in the 45th minute.
Alireza Kushki leveled the match with a header in the 55th minute.
Shortly afterwards, Persepolis put their Great Clergy under pressure, and the unmarked Ali Alipur won the winner in 71 minutes with a right-footed strike.
There were 105 meetings between the rivals, with Persepolis leading with 29 wins and Estegral 26. 50 matches being played.
Earlier in the day, PGPL leader tractor and Sepahan shared the loot in a goalless draw at Yadegar Stadium in Tabriz.
Additionally, Mes defeated Chadormalou 1-0 with Rafsanjan, and Esteghlal Khuzestan lost to Malavan 2-1 with Ahvaz.
The tractor leads the table with 45 points, one point above Sepahan. Persepolis is third with 41 points.
MP/TT