As many as 78 flights by the country's largest carrier Cebu Pacific were cancelled, affecting nearly 14,000 passengers, the company said in a statement.
Flag carrier Philippine Airlines also said some of its flights were cancelled or delayed but could not immediately say how many.
The blackout hit Terminal 3, which services mostly domestic flights, late on Saturday and power was not restored until before dawn on Sunday.
Exhausted passengers sprawled on the floor as check-in counters and luggage carousels shut down.
Long queues formed outside the terminal as entrances were closed until power was restored.
Terminal 3 of Ninoy Aquino International Airport, named after the assassinated father of incumbent President Benigno Aquino, handles an average of 350 domestic and international flights daily, according to data from the transportation ministry.
It is one of four terminals in a complex that was once dubbed by the travel website Guide to Sleeping in Airports as the world's worst due to leaking toilets and creaking facilities.
"We are looking into the root cause of this problem," Terminal 3 general manager Octavio Lina told DZMM radio.
Manila power retailer Meralco said a transmission line tripped briefly but was restored in minutes, suggesting that the problem could be with the airport's systems.
The four Manila airport terminals were designed for 17 million passengers annually, but overuse has made the airport notorious for flight delays.
Plans to build a new airport outside Manila have not materialized under Aquino. An excruciatingly slow infrastructure overhaul has led to chronic commuter train breakdowns and traffic jams.
Philippine Airlines (PAL), a trade name of PAL Holdings, Inc. (PSE: PAL), also known historically (until 1970) as Philippine Air Lines, is the flag carrier of the Philippines.
Headquartered at the PNB Financial Center in Pasay City, the airline was founded in 1941 and is the first and oldest commercial airline in Asia operating under its original name.
Out of its hubs at Ninoy Aquino International Airport of Manila and Mactan-Cebu International Airport of Cebu, Philippine Airlines serves 31 destinations in the Philippines and 41 overseas destinations in Southeast Asia, East Asia, Middle East, Oceania, North America and Europe.