Aleksandar Mitrovic opened the scoring for the visiting team with a header in the 18th minute.
An altercation between Vahid Mohammedzadeh and Mitrovic following an aerial duel developed into a brawl which prompted the referee to send off Al Hilal captain Salman Al Faraj and Nassaji’s Amir Houshmand seven minutes before the interval.
Neymar scored Al Hilal's second goal in Tehran’s Azadi Stadium in the 58th minute and Saleh Al Shehri scored the third goal in the added time.
Al Hilal will next host Mumbai City, while Nassaji look to make amends when it travels to Uzbekistan to face Navbahor on Matchday Three.