Reza Shakari put the visiting team ahead in the 30th minute from the penalty spot.
Mehdi Ghaedi made it 2-0 in the 36th minute from a set-piece.
On November 22, Iran had lost to Qatar 2-1 in a friendly match held in Doha’s Lusail.
The match was the last warm-up game for Hamid Estili’s side ahead of the AFC U-23 Championship Thailand 2020.
Iran is paired in Group C of Thailand 2020 alongside China PR as well as South Korea and the defending champion Uzbekistan.
The young Team Melli will open the campaign with a match against Uzbekistan on January 9.
Thailand 2020 also serves as qualification to the Tokyo 2020 Olympics, where the top three teams, aside from host nation Japan, will represent Asia.