The youth players of coach Johny Tam clobbered Giordano, 74-65, while the First Fivers nipped San Beda-Toprite, 89-87, in the crossover semifinals to earn berths in the one-game championship round.
FedEx actually trailed Giordano, 57-58, in the final 2:20 but Mark Pingres strung up six straight points to key the Nationals fightback.
Pingres finished with eight points, all in the final three minutes, while Elvis Tolentino and Archer Calacar had 14 apiece for FedEx in this 12-day cagefest sanctioned by the Basketball Association of the Philippines.
In the other game, Mark Piodo capped a night-high 26 points with a 20-footer for the First Five game-winner in the final 12 seconds.
Piodos brother Marlon backed him up with 12 points while veterans Aldrin Morante and Eric Ramirez combined for 31 markers.