Angel Guirado was a goal away from a hat trick as he scored for the Azkals in the seventh minute and in the first-half injury time.
The Fil-Spanish scored on a header just before halftime as he connected with Dennis Cagara, who delivered a fine free kick.
Guirado opened up the scoring for the Azkals, who finally notched a victory in the series of international friendlies, with a curling effort.
Carli de Murga doubled the Philippines’ early edge, 2-0, with a goal in the 12th minute.
The Philippines was held to back-to-back draws against Malaysia and Indonesia in the past matches.