Ryunosuke Yada opened the scoring for the Japanese team just 10 minutes into the match and Kohei Mochizuki made it 2-0 four minutes later.
Ryunosuke Sato scored Japan’s third goal from a free-kick in the 74th minute.
Iran will now face loser of Korea Republic and Uzbekistan on Sunday at the Pathum Thani Stadium.
Iran had already secured a berth in the FIFA U-17 World Cup Indonesia 2023.