The 18-year-old Agojo coasted along with a four-under-par 68 but that was enough to turn back Villaromans stunning nine-under-par 63 at the sun-baked Pueblo de Oro.
Agojos 66-66-68 worth 178 points gave her a winning seven points over Villaroman, who did 73-71 the first two days for 171 points in the Molave scoring system.
With Agojo claiming her second major crown in two months after her Philippine Ladies Open victory last month, Villaroman, the 1999 champion, settled for the Championship Division title.
Runner-up was Anya Tanpinco (68-165) and third was Korean Kim Cho Hui (72-161).
Lina de Guzman, the 1993 and 2002 champion, was fourth (69-159) and defending champion Lora Roberto (76-157) was fifth.
With a 12-point margin going to yesterdays final round, Agojos win was never in doubt despite Villaromans torrid round that saw her snare two eagles and six birdies against a lone bogey.
Agojo showed a brave heart and rock-solid confidence in turning back the challenge of Villaroman, even finishing birdie-birdie after Villaroman eagled 17.
"No, I was never worried with her game," said Agojo of Villaromans round.
"I knew my first two rounds were more than enough to carry me through.
Besides, napakalaki ko nang tanga pag natalo pa ako with that 12-point margin going to the last round."
The tournament, began in 1964 by the National Golf Association of the Philippines, gives four points to a birdie, three to a par and two to a bogey.
"Before the start of todays round, I made up my mind that I wouldnt collapse," said Agojo. "So, when Milette (Villaroman) eagled No. 5 and I made birdie, I knew my game would hold."
Despite her scorching game, the closest Villaroman got to within Agojo was seven points after 15 when Carmelette scored her sixth birdie for the day.
"I dedicate this victory to my parents and my entire family," said Agojo, the youngest of 10 children. "Its a dream come true as I have now won the three majors, including the Philippine Ladies Open and the DHL-NGAP Open."