Dragan Ceran gave Pakhtakor the lead in the 28th minute at the King Abdullah Sport City Stadium in Buraidah, Saudi Arabia.
Shahriyar Moghanlou equalized the match in the 49th minute and doubled the scoreboard six minutes later.
Mohammad Reza Hosseini made it 3-1 in the 70th minute.
On Sunday, Pakhtakor faces group hosts Al-Taawoun while Moharram Navidkia’s men face Qatar’s Al-Duhail.