A penalty from Hadi Aghlili and Kianoosh Rahmati's 85th minute strike helped Iran retain the title in front of 10,000 fans at the Azadi Stadium.
Jordan had equalised through Amir Deeb in the 80th minute and ended the game with ten men following the dismissal of Mohammad Alkasim for a second yellow.
Iranian coach Ali Daei said, "It was a very difficult game against Jordan."
"We had a good performance and possessed the ball more than them. My goal in this tournament was to give an opportunity to the young players and I congratulate them on their attitude."
Jordanian coach Nelo Vingada said: "I congratulate the Iranians for this victory and I am pleased that we lost the game by only one goal. It's difficult to play Iran in a final especially with one man short. But my players put up a very good performance."