In the match, held at the Jakarta International Stadium in Jakarta, Indonesia, Abolfazl Zamani put the Iranian team in the lead in the 31st minute.
Reiss Russell-Denny equalized the match in the 63rd minute and Joel Ndala scored the winner in the injury time.
Iran is scheduled to face New Caledonia on Friday.
Hossein Abdi’s men had defeated Brazil 3-2 in its opening match in Group C.