The Wonju DB Promy guard drained the go-ahead trey before following it up with a tough layup to put the hosts up, 104-100 with 1:31 remaining.
Dwight Ramos kept the Philippines in the thick of things with a dunk with 14.5 seconds left, but Kang Sang-jae iced the game at the free throw line with 8.3 ticks remaining.
Heo led Korea with 21 points on 5-of-9 clip from distance, alongside eight dimes.
It's much like a repeat of Friday's 96-92 win for Korea where it denied the Filipinos' late rally.
This time, the Philippines crawled back from an 82-74 deficit heading into the fourth period and even took a 100-99 lead on a four-point play from Rhenz Abando with 2:41 on the clock.
But that only paved the way for Heo's heroics down the stretch to sweep the two-game series.
Ramos starred for Gilas with his 31 points, 10 of which coming in the payoff period, to go with eight rebounds and three assists.
Abando also impressed with his 19 points from a 4-of-6 clip from deep, alongside five boards and two dimes, RJ Abarrientos sunk five treys for his 17 points and three rebounds, and Carl Tamayo got 12 points and six assists.
It was a solid showing from the boys of coach Nenad Vucinic with the Filipinos dishing out 31 assists in the game, flashing promising signs heading into the third window of the 2023 Fiba World Cup Asian qualifiers.
Lebron Lopez, though, sprained his right ankle after a bad landing in the second quarter.
Ra Gun-A, also known as Ricardo Ratliffe, produced a double-double of 27 points, 18 rebounds, and three assists, while Yeo Jun-seok had 17 points and six boards for Korea.
KOREA 106 -- Ra 27, Heo U 21, Yeo 17, Lee DS 14, Choi 9, Kang 8, Heo H 5, Kim 5.
PHILIPPINES 102 -- Ramos 31, Abando 19, Abarrientos 17, Tamayo 12, Belangel 7, Ravena 6, Navarro 4, Chiu 2, Quiambao 2, Lopez 2.
Quarters: 25-29, 47-53, 82-74, 106-102.