The complaint adds another layer to Qatar's progression to Friday's final of the continental football showpiece in the UAE, which is part of a quartet of nations boycotting Doha diplomatically and politically.
"The Asian Football Confederation has received a protest from the United Arab Emirates FA regarding the eligibility of two Qatar players," the governing body said in a statement on Thursday.
"This protest will now be reviewed in line with the AFC regulations."
The complaint about Qatar's Almoez Ali, a 22-year-old striker born in Sudan, and Bassam Al Rawi, a 21-year-old defender born in Iraq, was reportedly filed within two hours after Qatar's victory over the UAE.
It is alleged the Al Rawi and Ali have not met residency requirements to be eligible. Qatar states they have relatives born in the country which allows them to play which the UAE dispute.
The United Arab Emirates FA were given 48 hours to provide evidence, the Abu Dhabi-based The National newspaper reported.
Football fans on social media denounced the move by the UAE, calling the timing of the complaint "curious, to say the least".
'Not on our minds'
The coach of Qatar's national team, Felix Sanchez said he was "not concerned at all" about the UAE's bid to get Qatar thrown out of the tournament.
"No worries about it," Sanchez told reporters on Thursday ahead of the final against Japan on Friday.
"We're here one more day, tomorrow we're playing one game and only focused on the game," he added. "Any other thing that's not related to the football point of view is not related to our minds at this moment."
Qatar has been the target of a land, sea, and air blockade by the UAE, Saudi Arabia, Bahrain, and Egypt since June 2017.
The quartet accuses Doha of supporting terrorism and opposition groups they have proscribed, charges Qatar vehemently rejects.
Qatari fans are not allowed to attend the fixtures in the UAE because of the ongoing ban on Qatari citizens entering the UAE.
Surplus tickets for Tuesday's semi-final were bought out by Emirati government-linked bodies and distributed to "loyal" local fans, meaning The Maroons (Qatar's national colour) were up against a stadium full of hostile onlookers.
Qatari players were filmed being struck by and dodging slippers, shoes, and bottles thrown by local fans after scoring their second goal.
In a statement sent to Al Jazeera, the AFC said it was "conducting a thorough investigation into events at the Asian Cup UAE 2019 semi-final between the United Arab Emirates and Qatar".
"Once that investigation has been completed the AFC will decide on the appropriate next steps," it added.