The hot shooting that helped St. Bonaventure average 90 points in its first two games of the Paradise Jam Tournament disappeared during the final game on Monday.
Brigham Young held Bona to 28 percent shooting from the floor in a 66-57 victory.
"They contested every shot that we took," Bona coach Jan van Breda Kolff said. "Everybody was pressing a little bit. And we just weren't making shots. Even considering how poorly we shot, we still had a chance, but just couldn't get some key plays down the stretch."
The Bonnies missed their first six free throws of the second half, and the Cougars took advantage and went ahead, 37-34.
Marques Green, the tournament MVP, then led his team back with seven points as the Bonnies went on another run halfway through the second half to regain the lead, 45-43.
Green had seven points during a 9-2 run by the Bonnies that tied it at 57, before the Cougars went on their game-ending spurt.
"BYU is the most fundamentally-sound team we'll play this year. You have to give them a lot of credit," said van Breda Kolff.
Green led the Bonnies (2-1) with 19 points and Mike Gansey added 10 first-half points. Green averaged 20.7 ppg. for the three games.
The Bonnies advanced to the final after wins over Michigan on Saturday (89-68) and Virginia Tech on Friday (91-78). Bona shot a combined 47 percent in those games.
Jared Jensen had 15 points to lead BYU. Travis Hansen had 12 points, and Mark Bigelow added 11 for the Cougars, who closed with a 9-0 run to seal the win.