Shayan Mosleh, who came off the bench in the last minutes, scored the winner in the dying moments of the match.
With one game in hand, Persepolis moved back to top of the table with 27 points, two points clear of Pars Jonoubi.
“I am so happy because we have defeated one of the best Iranian teams. I had already told my players Pars Jonoubi are a hard-working, competitive and disciplined team. To create scoring chance against the team is very difficult,” Persepolis coach Branko Ivankovic said in the post-match news conference.
“I think we were the better team and deserved to win the match. I congratulate this win to my players for believing that the win was possible,” the Croat added.
It was the Blues’ fourth win in the current season after 13 weeks.
Elsewhere, Zob Ahan suffered a 1-0 home loss to Foolad.