Almoez Ali struck in Doha to send Qatar into their second straight final, further exorcising the demons of their first-round exit at the 2022 World Cup.
Sardour Azmoun gave Iran the lead in the fourth minute before Qatar equalised soon after when Jassem Gaber's shot went in via a heavy deflection.
Qatar's Akram Afif then notched his fifth goal of the tournament with a wonderful strike minutes before half-time, only for Iran to equalise through an Alireza Jahanbakhsh penalty early in the second period.
Match-winner Ali scored an Asian Cup-record nine goals to lead Qatar to their first title in 2019 but he had managed only one heading into the semi-finals of this year's tournament.
His late strike was worth the wait for Qatar, and ended Iran's bid for a first Asian title since 1976.