Iran still had Hong Kong to thank for beating Syria 2-1 to help Abbas Chamanian’s boys finish second to North Korea in Group A and progress as one the five best runners-up.
Iran started on the front foot in Zarqa’s Prince Mohammed Stadium and took the lead through host captain Karzg Shadi Alqasem’s 15th-minute own goal.
Already eliminated after suffering three defeats, Jordan fought back to draw level through defender Nour Aldeen Amro in the 37th minute with forward Mohammad Mustafa Aburomeh putting the home side ahead three minutes later.
Iran, however, managed to turn things around late in the game, with defender Abolfazl Kazemi netting the equalizer in the 71st minute.
Salman Ghaffari restored Iran’s lead six minutes later before Mehrdad Aqa Mohammadi’s spot-kick deep into stoppage time confirmed the points for Chamanian’s side.
Later in the day, Abdulrahman Dinawai put Syria in front in the 64th minute, only to see his strike canceled out by Hui Siu Chung a minute later.
Midfielder Jeffery Chin struck the decisive winner in the 88th minute.
Iran began its qualification campaign with a 7-1 rout of Hong Kong but fell to a shock loss to North Korea, which went on to win the group with a clean sweep of four wins.
Chamanian’s boys bounced back to beat West Asian champion Syria 1-0 before Sunday’s triumph to conclude the qualifiers with nine points.