With the Robert Trent Jones-designed layout spared by the heavy downpour that swept the metropolis but played long with soft and muddy fairways, Pagunsan came up with a decent round as he virtually put the wraps on the coveted crown in the 72-hole tournament.
Carmellete Villaroman carded a four-over-par 76 and totalled 227 as she beat Heidi Chua (77) and Ruby Chico-Walker (78) by three strokes for the ladies championship.
After three rounds in the mens championship, Pagunsan, who established a course-record eight-under 64 in the second round, had a seven-under 209, seven strokes up on first-round leader and fellow Canlubang bet Solomon Gines.
Gines, a former member of the national team, matched par 72 as he surged past Wack Wacks Marlon Dizon to seize second place with a 216. Dizon fell 10 shots off the face following a fat 76 for a 219.
Ronnie Torrecampo also of Canlubang shot the days best score of one-under 71 to gain solo fourth place with a 220.
Marvin Dumandan and Jay Bayron, Pagunsans teammates in the RP team bound for the Kuala Lumpur SEA Games next month, came next at fifth and sixth place after a 73-225 and a 75-226, respectively.
Canlubang mainstay Rolly Viray tied Bayron at 226 after a 77. The tournament is backed by Globe Telecoms and leading British pro George Walker, one of the supporters.