Pagunsan toured the Sungai Long Golf and Country Club for a one-under-par 71 and won pulling away as his chief rivals failed to mount serious threats against the 21-year-old Negrense.
He finished with a nine-under 279 for a remarkable nine-stroke win over Malaysias Airil Rizman in successfully defending the title won by Gerald Rosales now a professional campaigning in the Asian Tour in Brunei in 1999.
The Philippines, however, failed to win even the bronze in the womens play as third-round leader Carmellette Villaroman succumbed to championship pressure, limping with a 79 for 224, and yielding the gold to Thai Onnarin (69-217).
Struggling to a 41 in the back nine the start of her final round, Villaroman likewise bungled a shot at the bronze medal with a bogey-bogey finish. Teammates Heide Chua and Ruby Chico Walker wound up 74-225 at ninth and 78-232 at 13th, respectively.
The silver went to another Thai bet Titiya Plucksataporn (74-220) and the bronze to Malaysias Sitti Retno Purwandi (76-223).
But the Philippines rejoiced as Pagunsan stamped his class in the mens class, hacking out the most impressive victory in SEAG golf in years and, later, receiving his gold medal from no less than Sultan Tuanku Jaafar, one of the countrys 14 sultans.
The 2000 World Amateurs veteran had earlier rounds of 67-74-67.
Jay Bayron won day honors with a four-under 68 and finished 11th at 297. Marvin Dumandan also improved with a 72 for 304 while Joselito Zaragoza scored a third-straight 76 for 306.
"Weve won the individual gold and I think we can also be a good contender in the team event with our other players now shooting low scores," said National Golf Association of the Philippines executive director Jake Ayson.
The golfers take a rest today before figuring in the team competition, using the match-play format, tomorrow. The teams will field three players each in best-of-three matches.
Philippine coach Iggy Clavecilla said hell announce his bets only minutes before the opening round but stressed all his players are ready to do battle. He said: "Mas gumanda ang chance natin with the match-play format kasi iyung mga rookies natin sumasabog ng malaking butas pero pwede kang balikan ng dikit-dikit na birdies."
Scoring birdies after birdies is something which Pagunsan has done here except yesterday when he played a bit cautious.
Nonetheless, Pagunsan came up with a solid round, firing two birdies against one bogey which he got for overshooting the green in the par-3 No. 3. His chip shot rolled one pin away from the cup then he two-putted for that bogey.
But he quickly made up for it on the par-5 No. 5 which he earlier thought could be his waterloo in this Jack Nicklaus-designed layout. Facing a tight fairway bordered by water on the left and out-of-bounds on the right, Pagunsan opted for a three-iron. His tee-shot sailed onto the center of the fairway and he made it to the green in two for the birdie.
On the green, the Thai gallery made a big applause as second-round co-leader Wisut Artjanawat, running second before the last round, one-putted from 12 feet. The Filipino crowd likewise cheered wildly as Pagunsan made a birdie-putt practically from the same distance.