Tajikistan topped Group D with six points, one ahead of DPR Korea who drew 2-2 with Oman in a match played simultaneously.
Tajikistan - the 2018 runner-up - also qualified for the FIFA U-17 World Cup Qatar 2025 and will take on Group C runner-up Korea Republic in the knockout stage.
Both teams needed victory to stand a chance of advancing.
Mekhrubon Odilzoda was on target for Tajikistan in the 12th minute at the Prince Abdullah Al Faisal Stadium.
Champion in 2008, Iran drew level when Omid Gharahchomaghloo found space on the right in the 52nd minute and drilled a low shot past Abubakr Rahmonqulov.
Tajikistan regrouped and scored its second in the 67th minute after Shoev collected a through ball from Odilzoda and sent a shot from close range that rocketed past Khalilian.
Boosted by the goal, Tajikistan continued applying pressure and Abdullo Ibragimzoda put the match beyond doubt when he picked up the ball on the edge of the box and scored in the 89th minute.