Iraq were playing their second match in Dubai after sharing a 0-0 draw with Jordan last Thursday while Vadim Abramov's men suffered their second consecutive defeat after losing 1-0 to Syria.
Uzbekistan were dominant in the first half and nearly went ahead in the 17th minute but Azizjon Ganiev's free-kick just missed the mark.
However, they opened the scoring in the 39th minute when Khojimat Erkinov was fouled inside the area by Iraq goalkeeper Mohammed Hameed, who was then beaten by Dostonbek Khamdamov's spot-kick.
Khamdamov nearly made it 2-0 two minutes later with a powerful shot from just inside the area but Hameed cleared the ball for a corner.
Iraq pushed forward in the second period and nearly leveled the scores in the 52nd minute but Ibrahim Bayesh's shot from distance was blocked by Uzbekistan goalkeeper Abduvohid Nematov.
Iraq eventually equalised after a mistake from Nematov who failed to handle Mohanad Ali's shot from inside the area three minutes after the hour mark.
The Iraqis scored their second five minutes before the end when Mazin Fayyadh was fouled by Rustamjon Ashurmatov in the penalty box with Iraq captain Ali Adnan making no mistake in slotting the ball under Nematov.
Friendlies Matchday 1