The QF19 flight was travelling from Sydney to Manila on Sunday afternoon when local authorities closed the airspace, forcing the plane to return to the NSW capital.
It was flying over Queensland's north coast, just below Papua New Guinea, when it made the U-turn.
The Airbus A330 was refuelled at Sydney before re-departing for Manila, arriving in the early hours of Monday local time.
"All airlines were prevented from arriving into Manila on Sunday afternoon as local authorities closed the local airspace," a Qantas spokesperson said in a statement.
"This meant our flight from Sydney had to turnaround."
A power outage caused the closure of the airspace at Ninoy Aquino International Airport, prompting more than 360 domestic and international flights to and from the airport to be delayed, cancelled or diverted.
Transportation secretary Jaime J Bautista said the problem began when the the country's air traffic control centre lost communication, radio, radar, and internet because of the power outage.
He apologised for the inconvenience and said authorities were working to assist affected passengers.
The turnback follows Qantas' budget carrier Jetstar apologising last week after a flight from Melbourne to Bali was turned back hours after take-off because of a miscommunication with Indonesian authorities.
A United Airways flight from Los Angeles to Sydney was also forced to make an emergency landing at Pago Pago International Airport in American Samoa on Friday morning (local time) due to a mechanical issue.
It meant hundreds of passengers aboard the Boeing 787-9 missed out on taking part in New Year Eve celebrations in Sydney after crossing the dateline too late.
With Reuters and AP
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