Syria's Fahd Youssef saw his penalty saved by goalkeeper Alireza Beiranvand in the shootout while Iran converted all their spot kicks, with skipper Ehsan Hajsafi netting the decisive one.
Iran were one of three teams to finish the group stage with maximum points and knockout stage debutants Syria had done well to contain them until they gifted their Middle Eastern counterparts a penalty in the first half.
Aiham Ousou deliberately barged into Mehdi Taremi without making any attempt to go for the ball and the Iranian striker stepped up to take the penalty, firing the spot kick into the bottom-right corner for his third goal of the tournament.
But Syria levelled when Pablo Sabbag came on as a substitute and immediately won a penalty when he beat the offside trap and was fouled by Beiranvand, with Omar Khribin calmly slotting it home to make it 1-1.
Things went from bad to worse for Iran when Taremi was sent off for a second yellow card. Having been booked for simulation earlier, Taremi fouled Alaa Al-Dali to earn another booking and reduce Iran to 10 men for the final minutes and extra time.
However, Iran managed to hold on and take the game to penalties where they were unfazed by the pressure, extending coach Amir Ghalenoei's unbeaten run to 15 games since he took charge of Team Melli in March last year.
