Ahead, 9-8, at the start of the final frame, center forward Ali Alamara made a goal in the last 5:37 and his brother Norton fired back-to-back goals to give the hosts enough cushion en route to the victory.
Indonesia did score two goals through Henrian Saragih and Hendri Maciano but the Filipinos hung tough to preserve the win.
"We just studied well our offensive patterns and worked on our defense perfectly," said coach Reynaldo Galang. "I also credit the team’s endurance and stamina. It helped us to overcome our opponent’s physical game."
Earlier, center forward Monsuito Pelenio scored RP’s first three goals to put RP ahead 3-2, 2:12 left in the first frame.
Frazier and Norton Alamara collected two goals each to lead the water polo team.
The Filipinos, who settled for the bronze medal in the last SEA Games in Vietnam in 2003, will battle defending champion Singapore today at resumption of action in one of the three aquatics events lined up in the next three weeks, the two others being swimming and diving.