Mehdi Taremi was brought down by the Syrian defender and he converted the penalty with a right-footed shot in the 34th minute at the Abdullah bin Khalifa Stadium in Doha, Qatar.
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 goalkeeper Alireza Beiranvand, with Omar Khribin calmly slotting it home to make it 1-1 in the 74th minute..
The condition went from bad to worse just after the 90th minute after Taremi received his second yellow card.
Team Melli won 5-3 in the shootout after the match had ended 1-1 after extra time, extending coach Amir Ghalenoei’s unbeaten run to 15 games since he took charge of Team Melli in March last year.
Syria’s Fahd Youssef saw his penalty saved by Beiranvand in the shootout while Iran converted all their spot kicks, with skipper Ehsan Hajsafi netting the decisive one.
Iran will meet Japan on Saturday in the competition’s quarterfinals.
Iran had stormed to the top of their group with three wins, finishing ahead of the United Arab Emirates in second but Syria finished third in their group behind Australia and Uzbekistan.