Mehdi Jafari was on target for Iran in the 57th minute but Mohammad Javad Hosseinnejhad was sent off in the 76th minute.
Iran suffered two goals in the added time.
The event has brought Kyrgyzstan, Bahrain, Iran, and Russia at the Kurmanbek Stadium together.
Iran, who lost to Russia 2-0 in its opening match, will play Bahrain on Tuesday.
All participants in the games prepare for the 2026 AFC U-23 Asian Cup final tournament, which will be held in Saudi Arabia in January.