Persepolis started the tie on the front foot and had its first look at goal after 10 minutes but Ahmad Noorollahi sent his free-kick straight into the arms of FC Goa custodian Dheeraj Singh.
FC Goa gradually grew into the match and was rewarded in the 14th minute when Edu Bedia rose high to nod home Brandon Fernandes’ free-kick to register a historic moment for the Indian club.
Persepolis, however, came back fighting and equalized when Mahdi Torabi sent Dheeraj Singh the wrong way from the spot in the 18th minute after Isa Alkasir had been brought down inside the box.
Persepolis increased its intensity of play and captain Seyed Jalal Hosseini scored his second goal of the campaign when he angled his header into the back of the net following Torabi’s cross from the left flank.
Dheeraj Singh, FC Goa’s star in the 0-0 draw with Al-Rayyan on Matchday Two, was at his best in the 42nd minute to deny Hossein Kanaani from the penalty spot following a foul on Ehsan Pahlavan.
The two sides will meet again on Friday with Yahya Golmohammadi's team aiming to take a step closer to the Round of 16 while FC Goa will surely relish another go at Persepolis.