Mehdi Ghaedi scored the winner before the halftime at the Hazza bin Zayed Stadium in Al Ain.
The UAE had a late opportunity to level proceedings from the spot after referee Kim Jong-hyeok pointed to the spot for a handball by Hardani but upon VAR review, it was overturned and with that, the Emiratis’ hopes of a comeback ended.
Iran had defeated Kyrgyzstan on September 5 in Tehran.
Leader Uzbekistan will host Iran on October 10 in Tashkent.