Japanese winger Yukiya Sugita opened the scoring for the visiting team in the 16th minute and Danial Esmaeilifar and Ashkan Dejagah were on target on 43rd and 66th minutes, respectively.
Earlier on the day, Persepolis defeated Esteghlal 1-0 to stay top of the table.
On Sunday, Sepahan will host Naft Masjed Soleyman in Isfahan and Zob Ahan will play Sanat Naft in Iran's southern city of Abadan.
Persepolis remains top of the table with 48 points, followed by Tractor Sazi (46 points), Esteghlal (43 points) and Sepahan (43 points).