Nima Andarz and Mahan Sadeghi were on target in the 18th and 19th minutes.
Iran started the campaign with a 6-1 win over Afghanistan in Group B but was held to a goalless draw against Qatar.
Afghanistan also defeated Qatar 2-1 in the group.
Iran is scheduled to play Yemen on Sunday, while South Korea will meet host Thailand.
Iran will qualify for the 2023 FIFA U-17 World Cup if it defeats Yemen.