After trailing by as much as 16 points in the opening period, Kiefer Ravena led the Gilas' comeback along with Troy Rosario to take a 34-22 lead early in the second period.
Gilas led by as many as 15 in the third quarter, courtesy of baskets from Andray Blatche, Jayson Castro and Calvin Abueva, until the Japanese cut the deficit to two, 86-84, with 30 seconds remaining.
Castro helped the Philippines secured the victory with a floater with 10.6 seconds left to put Gilas ahead, 88-84.
Blatche, who finished with team-high 18 points and 16 rebounds, sealed the game with a split from the free-throw line for the final score.
Rosario and Ravena contributed 14 and 13 markers, respectively, off the bench.
Castro had two three-pointers and tallied eight points and three assists.
Abueva, the most efficient player for Gilas with a plus-minus of +20, added 8 points, 3 rebounds, two assists and a steal in only 10 minutes of action.
Makoto Hiejima led Japan with 23 points, 4 rebounds, and 2 assists for the match.
PHILIPPINES 89 - Blatche 18, Rosario 14, Ravena 13, Norwood 8, Castro 8, Abueva 8, Fajardo 7, Pogoy 6, Aguilar 5, Jalalon 2, Wright 0, Maliksi DNP.
JAPAN 84 - Hiejima 23, Brown 16, Tanaka 12, Shinoyama 9, Tsuji 8, Ota 6, Takeuchi 5, Uto 3, Harimoto 2, Furukawa 0, Hashimoto 0.
Quarters: 21-22, 46-41, 72-61, 89-84.