Qatar's last two scorers -- captain Hassan Al-Haydos and Hamid Ismail -- were also the target of missiles at the Mohammed bin Zayed Stadium in Abu Dhabi.
The AFC said the UAE FA was penalised under a number of articles under its disciplinary code, including liability for spectator conduct (article 65) and organisation of matches (article 64).
"The AFC Disciplinary and Ethics Committee has sanctioned the UAE FA with a fine of $150,000 following the incidents that occurred during their Asian Cup semi-final match against Qatar," Asian soccer's governing body said in a statement.
"In addition, the UAE FA has also been ordered to play one match without spectators... which will come into effect during their next match played on the territory of the UAE during the AFC Asian Cup 2023 (qualifiers)."
Fans had also jeered throughout the Qatar national anthem with dozens of Emiratis sitting for its duration before standing for the UAE anthem.
The UAE, Saudi Arabia, Bahrain, and Egypt cut political and trade ties with Qatar in June 2017 over allegations Doha supports terrorism, a charge that Qatar denies.
The AFC said the UAE FA must settle the fine within 30 days and warned it that any future violations may lead to more severe punishment.
Qatar sealed their first continental title with a stunning 3-1 win over four-times champions Japan in the final.
(Reporting by Shrivathsa Sridhar in Bengaluru)
