Team Melli came back from a goal down to win the match at the Saida Municipal Stadium in Sidon.
Soony Saad put the hosts into the lead in the 37th minute but Sardar Azmoun and Ahmad Nourollahi scored two goals in added time to keep Team Melli on top of the table.
Earlier in the day, South Korea edged the UAE 1-0 in Seoul.
Iran leads the table with 13 points, followed by South Korea with 11 points.
Dragan Skocic’s team will play Syria in Amman, Jordan on Tuesday and will move one more step closer to qualification if it defeats the Syrian team.