The Reds, who had defeated their arch rival Esteghlal 3-2 in the Tehran derby last week, lost 3-2 to Fajr-e Sepasi in a home game.
Mohammad Nouri gave Persepolis the lead in the 28th minute.
Mehrdad Karimian equalized the match nine minutes into second half with a long range shot. Two minutes later, Mehdi Rajabzadeh found Persepolis back of the net for the second time with a powerful strike.
Nouri scored his brace in the 70th minute with a header.
Persepolis keeper Hassan Hoshiar made a big mistake after he failed to save Ayyub Kalantari’s long range shot in the 87th minute.
Persepolis stays in 7th place in Iran Professional League standings table with 33 points.
Also on Tuesday, Shahin of Bushehr was held a 2-2 draw by Shahrdari in its home game.