Plastic water bottles pelted the turf and several shoes were hurled as Qatar celebrated the second goal in Tuesday's 4-0 rout of the tournament hosts in Abu Dhabi.
Akram Afif twice had to delay taking a corner as objects rained down, and Salem Al-Hajri was struck on the head after Qatar's third goal. One plastic bottle struck the crossbar behind Qatari goalkeeper Saad Al-Sheeb.
"The AFC (Asian Football Confederation) is conducting a thorough investigation into events at the (semi-final)," a spokesman told AFP.
"Once the investigation has been completed the AFC will decide on the appropriate steps."
Abu Dhabi authorities bought thousands of spare tickets and handed out them out to fans with Emirati identification, meaning the 42,000-capacity Mohammed Bin Zayed Stadium was nearly unanimously behind the home team.
Loud booing and whistling also drowned out the Qatari anthem before the game, which Qatar -- who will host the World Cup in 2022 -- dominated to reach their first Asian Cup final.
"Everybody knows about the problems but we don't care -- we just play football," Qatar defender Pedro Correia told AFP.
"Let the people talk, winning 4-0 is more important."