The 27-year-old ace opened up with consecutive 69s before pulling away from the field with a seven-under 65 in the third round on Saturday that set up the runaway win.
The low amateur in the recent Philippine Open at the Malarayat in Batangas, Pagunsan assembled another 69 on Sunday and padded a three-stroke overnight lead over Dott to as many as six going into the final six holes.
"Maganda ang kundisyon ng palo," said Pagunsan over the phone.
The entire RP National pool, captained by Villamor GM Bert Sabularze, was entered in the Pan West event, a 72-hole tournament where some of Asias best were in the field.
Jay Bayron finished at level 288 and Artemio Murakami totaled 291 as Team Philippines finished second, five strokes behind the rock-solid Australians 22-under tally.
Marvin Dumandan and reigning Singapore Amateur champion Michael Bibat finished respectively. Only Jun Bernis, the reigning RP Amateur champion, missed the 36-hole cut.
The six-man RP Team, meanwhile, will play its second straight tournament starting today in the Saujana Amateur Open at the Saujana Golf Club.
Dumandan finished a fighting second in this tournament last year.