The host team topped Group B with nine points, followed by Myanmar who secured six points after their second victory, beating Malaysia 4-0 in a match earlier.
Myanmar will play Australian Under-20 in the semi-final at Thong Nhat Stadium on May 8.
Any thought of the Philippines' early fightback evaporated in the fourth minute, when Nguyen Thi Minh Nguyet slammed home a rebound from Tran Thi Thuy Trang's earlier attempt.
Nguyet then went on to complete her hat trick, the second of Vietnam, in the 28th minute and a penalty kick 10 minutes later.
In between, Vu Thi Nhung scored in the 12th minute for the final scoreline.
Myanmar were all action on the field as they attacked the Malaysian fort from all angles. But the Malaysians were more determined, after their previous loss to Vietnam.
They regrouped well to control Myanmar for a long period and their frustration gave confidence to the Malaysians. But with a lack of pace upfront, it was always going to be a struggle for them to get their first goal of the competition.
Win Theingi Tun turned the Malaysian defence to shoot past keeper Asma Junaidi to open the score just two minutes to the interval.
And just a minute after the break, Asma's goal was breached again by Win Theingi who slammed home from close range.
But Asma did not lose focus and, despite a troubling knee, continued to play a pivotal role in restraining Myanmar, before caving in at the 69th and 75th minutes from striker Yee Yee Oo.
