The Reds, coached by Hamid Estili, lost the away match 2-1 at a packed Shahid Beheshti stadium in Bushehr late on Sunday, Mehr news agency reported.
The first half of the match ended scoreless with scarce opportunities as most of the game was played in the middle of the field.
Five minutes into the second half, Shahin Bushehr's Serbian player Ivan Petrovic made the best use of Persepolis' poor defense and opened the scoring on a long cross by Abbas Pourkhosravani from right.
Mansour Tanhaei then doubled the lead for Shahin, under Hamid Derakhshan, 21 minutes later through a header on a volley by Mohsen Hamidi.
Estili's men reduced the deficit nine minutes to the final whistle, when Mohammad Nosrati headed a cross from defender Sheys Rezaei inside the far post.
The Tehran-based club tried hard to level the game but their efforts turned out ultimately in vain as the Reds had to settle for the loss.
In another match of the day, Teraktorsazi downed Zob Ahan with a solo by German player Shpejtim Arifi in the 36th minute.
Three other matches were played out on Sunday, as Malavan and Rah Ahan tied nil-nil, Shahrdari and Saipa drew 1-1, and Foulad saw off Mes 1-0.