Ola Adeogun scored most of his points in the second half to finish with a game-high 23 on top of 14 rebounds and two blocks.
“It’s the composure and the calmness of the players plus we made the free throws,” said San Beda head coach Ronnie Magsanoc.
The Red Lions leaned on Adeogun in the closing minutes of the game, dumping the ball inside to the six-foot-eight center, who responded to the challenge.
Adeogun made two free throws that put San Beda back on top before Baser Amer sank one-of-two to pad on to their lead, 55-52, with 26.2 seconds remaining.
Jet Vidal, who knocked in a triple that knotted the count at 52, had a couple of chances for the Altas but on both times was off. Vidal, the graduating swingman, paced his team with 15 points.
Nosa Omorogbe also had 15 points.
Amer made it a two-possession game, 56-52, with only 16.3 ticks left.
San Beda will face either San Sebastian or Letran in a best-of-three championship series.
It wasn’t the kind of start the Red Lions wanted with 14 turnovers in the first half as the Altas, who even led by as much as nine, 26-17, in the third period, played far from being newbies on the big stage.
“When Nosa made the two triples I thought that was the game changer but we are able to face the challenge. The boys willed their way to coming back,” added Magsanoc. “The mission has always been the same for us which is to get to the top.”
Perpetual Help, which ended its eight-year Final Four drought, missed the contribution by Earl Thompson, who didn’t score in 19 minutes.