In the match held in Doha’s Abdullah bin Khalifa Stadium, Yuta Toyokawa (two goals) and Shoya Nakajima scored for the Japanese team in extra-time.
Iran almost salvaged a consolation four minutes from the end of the game, but Mohsen Karimi’s attempt came back off the bar before eventually ending in the arms of Masatoshi Kushibiki.
Japan is on the verge of qualifying for the Olympics for a sixth consecutive appearance.
Japan will meet either United Arab Emirates or Iraq in the next round, with the winner securing a place at the Olympics, while the loser will play-off against the other losing semi-finalist for the third and final spot in Brazil.
Iran has not qualified for the Olympic Games since 1976.