The limited flights out of Dubai and Abu Dhabi took place as the US State Department urged its own citizens in 13 countries, including UAE, Jordan, Saudi Arabia, Egypt, Lebanon and Oman, to "depart now via commercial means due to serious safety risks".
Sweeping airspace closures and flight cancellations across the region left many fewer options for heeding the advice.
Since US and Israeli strikes on Iran and retaliatory attacks on Israel and Gulf states started on Saturday, commercial flights have been halted or heavily restricted, leaving tourists, business travellers, migrant workers and religious pilgrims stuck in hotels, airports and aboard cruise ships.
Airspace remained closed Monday over Iran, Iraq and Israel.
Jordan instituted a temporary closure beginning Monday afternoon.
Other countries in the Gulf - including Qatar, Bahrain, Kuwait and Saudi Arabia - had partial or temporary closures that could be extended, according to flight-tracking service Flightradar24.
The service showed that after reports of Riyadh explosions from a drone, flights into King Khalid International Airport near Riyadh were holding or turning back.
About 13,000 of the roughly 32,000 flights scheduled into and out of the Middle East since Saturday have been cancelled, aviation analytics firm Cirium said.
Airlines operating evacuation flights are likely doing so with government backing, and the carriers' home countries may be assuming part of the financial risk, said Henry Harteveldt, president of travel market research firm Atmosphere Research Group.
"Airlines aren't going to resume operations until they are fully confident that there is a zero - or as close as possible to zero - risk that their aircraft will be attacked," Harteveldt said.
Long-haul carriers Etihad Airways and Emirates, based in Abu Dhabi and Dubai, along with budget carrier FlyDubai, said on Monday they would operate limited flights from the country, where air defence systems were deployed to intercept Iranian missiles and drones.
At least 16 Etihad flights left Abu Dhabi during a three-hour window on Monday, according to Flightradar24, heading to destinations including Islamabad, Paris, Amsterdam, Mumbai, Moscow and London.
The airline's website, however, said all its regularly scheduled commercial flights remained suspended until Wednesday afternoon.
Emirates said customers with earlier bookings would get priority for seats aboard the limited flights it planned to operate starting Monday evening.
FlyDubai said it would operate four outbound flights and five inbound.
Dubai Airports, the authority that runs the city's two airports, showed a larger number of flights on Tuesday but urged passengers to go to airports only if their airline had notified them with confirmation since operations remained curtailed.
The disruptions have been far-reaching because Gulf airports serve as critical global transit hubs linking Europe, Africa and Asia. Dubai International Airport alone handled a record 95.2 million passengers last year, making it the world's busiest airport when measured by international travel.
