In the match held at Jassim Bin Hamad Stadium in Group A, Qatar’s Ahmed Alaa and Abdelkarim Hassan scored in the 35th and 56th minutes respectively.
Iran captain Roozbeh Cheshmi missed a penalty in the second half to reduce the deficit.
Ali Karimi scored on the stroke of full-time for Iran, but it was not enough to deny the Qataris a victory.
Iran needs to win its final group match against China on Monday.
A total of 16 teams are battling for the three places available for Asian sides in Rio in Qatar from January 12 to 30 at four venues.