Arsalan Motahari, who joined Esteghlal in the January transfer window, scored twice for the Blues in this match.
He put Esteghlal into the lead in the 24th minute at the Azadi Stadium but Ali Alipour canceled out his goal five minutes later.
Motahari was on target once again in the 52nd minute.
Esteghlal had almost won the match but Persepolis’ Iraqi midfielder Bashar Resan found the back of the net from a tight angle in the 89th minute.
In Masjed Soleyman, Sepahan played out a goalless draw against Naft.
Persepolis sits top of the table with 41 points.
Sepahan is second with 36 points.
Esteghlal is third with 33 points.