Marvin Dumandan and Jun Bernis finished with 75 and the Filipinos pooled a 217 total for the day and an 866 total, way behind the Thais and seven shots off Myanmar for third spot.
It was the second-worst placing for the Filipinos in the event regarded as the official Southeast Asian team golf championship. The Philippines finished a dismal fifth in the 2002 edition.
The Thais rallied behind Wisut Artjanawats 69 and Chinarat Padungsils 70, nipping Malaysia in the run for home with a 210 for the day and an 837 tally, two shots clear of the Malaysians.
Wisut won the individual title with his efforts and Malaysian Ben Leong will remember this tournament for a long time after he missed a key chip on hole No. 16 for a double bogey 5 and a level 72.
Leong finished two strokes behind Wisut as he failed to defend his individual title by going two-over in the final two days. He went 10-under in the first two, including a scorching 65 in the second round on Wednesday.
Thailand scored a sweep of all titles at stake after its junior team completed a wire-to-wire performance behind Teerawat Paipong and hotshot Anujit Hinrunratanakorn.
Teerawat ran away with the individual tile despite a final day 74, winning it by three over Anujit with a 276 total even as Matthew Manotoc checked in fourth with a 287 after a 75.
The Philippine juniors also dropped down in the standings, settling for fourth spot with Laurence Negridos 73 and Tonlits Asistios 76 completing their 224 total for the day.
Thailand won the junior title by a whopping 31 strokes over Singapore. Malaysia finished third in the division with an 875 aggregate.