Joyce Semacio and Alisha Del Campo were on target in 47th and 52nd minutes, respectively.
Maryam Azmoun’s side refused to give up, launching a wave of attacks and pushing several extra bodies forward, but its efforts went without reward as the Philippines celebrated what may prove to be a priceless three points.
Earlier on the day, Chinese Taipei defeated Palestine 3-0.
Chinese Taipei will meet the Philippines in what looms as a crucial Matchday Two clash on Saturday, while Iran will look to keep its now slender hopes alive against Palestine.
In the final round, the successful sides of Group A, B and C, will join Australia, DPR Korea, Korea Republic, China PR and Thailand in two groups of four, with the top two teams from each group advancing to the play-offs.
The two winners from the play-offs will then qualify for the 2020 Tokyo Olympics with host and reigning Asian champion Japan.