Erfan Masoumi was on target for the host in the 29th minute but Persepolis captain Omid Alishah canceled out his goal in the 90th minute.
Issa Moradi scored the winner in the injury time to seal a 2-1 win for Kheybar.
Furthermore, Paykan lost to Aluminum 1-0 in Tehran, Zob Ahan and Foolad shared the spoils in a 1-1 draw in Isfahan, and Sham Azar lost to Fajr Sepasi 1-0 in Qazvin.