Paolo Hernandez waxed hot late with 13 points in the fourth quarter, including the insurance freebies and the dagger three in the last 36 seconds of the game.
He finished with 22 points on 3-of-9 shooting from deep, to go with eight rebounds, five assists, and two blocks as the Cardinals recovered from a 6-19 first quarter deficit and used a killer 29-point finishing kick to complete the turnaround.
Adrian Nocum had 12 of his 17 points in the final period, on top of four boards, while Jasper Salenga got 14 points, four rebounds, and three steals.
Mapua ended its campaign at 7-11, an underwhelming finish for last season's runner-up.
Ichie Altamirano had a season-high 24 points, hitting four 3-pointers, on top of four boards, three assists, and two steals, but can't make the crucial buckets as the Golden Stags ended their season at 8-10.
Romel Calahat had a 13-point, 15-board double-double for San Sebastian.
Mapua 75 - Hernandez 22, Nocum 17, Salenga 14, Bonifacio 7, Agustin 5, Cuenco 3, Igliane 3, Pido 2, Soriano 2, Garcia 0, Mercado 0, Gamboa 0, Lacap 0.
San Sebastian 67 - Altamirano 24, Calahat 13, Are 9, Una 8, Aguilar 4, Villapando 2, Sumoda 2, Escobido 2, Suico 2, Paglinawan 0, Concha 0, Cosari 0.
Quarterscores: 6-19; 29-32; 46-51; 75-67.