The two teams had met in the semi-finals of the previous edition, with Japan emerging 3-0 winners and they looked on course to repeat the win when they took the lead before the half-hour mark, but two second-half goals from Mohammad Mohebi and Jahanbakhsh turned things around for the Iranians at Education City Stadium.
Captaining Team Melli on the day in the absence of Ehsan Hajsafi, Jahanbakhsh nearly opened the Iranians' account in the 13th minute when he picked up Saeid Ezatolahi's pass down the left flank and curled a shot that nearly caught goalkeeper Zion Suzuki off-guard, but fizzed just over the crossbar.
The first test for Suzuki came after 18 minutes when Hidemasa Morita lost possession on the edge of the Japanese penalty box, allowing Ezatolahli to control the ball and hit with his left, but his shot was too central and the Japanese goalkeeper had no problems in dealing with it.
Morita more than made up for his mistake 10 minutes later. The central midfielder embarked on a solo run to beat three Iranian defenders and arrive into the box before drilling an effort that made its way into the back of the net despite goalkeeper Alireza Beiranvand's best efforts to make the save.
Iran's biggest chance to equalise before the break was a Saman Ghoddos half-volley after he controlled the ball with his chest, but the Brentford midfielder narrowly missed the target.
Nine minutes after the restart, Team Melli were able to restore parity after a long pass from Suzuki was interrupted and the ball fell to Sardar Azmoun who supplied a through pass to Mohebi. The forward was left with just the goalkeeper to beat and coolly slotted into the bottom corner for the equaliser.
Iran thought they had completed their comeback in the 64th minute when Azmoun latched onto a long ball, dribbling expertly past two defenders and powering past Suzuki into the near post, but the AS Roma forward had strayed marginally offside and the goal was overruled.
The Japanese goalkeeper was called into action again to stop a spectacular Ezatolahi volley from the edge of the box and confidently produced the required save with just six minutes left to the end of normal regulation.
Deep into four minutes of added time, Iran got a golden chance to win the game when Ko Itakura brought Hussein Kanaani down inside the box.
Jahanbakhsh stepped up and emphatically dispatched it into the top corner to earn head coach Amir Ghalenoei's side the all-important victory.
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