Justin Benedetti added 15 points for Bellarmine (33-2), which had five players score double figures.
"It's the best feeling in the world," Benedetti said. "Our team worked hard all year long. We just wanted to show the world how we play Bellarmine basketball, and let's do it together."
Tsung-Hsien Chang led BYU-Hawaii (22-9) with 35 points, the fourth most in championship game history, after scoring 43 in the semifinal to earn Most Outstanding Player honors for the tournament.
It was the first appearance for both teams in the Division II championship game.
Braydon Hobbs and Luke Sprague each added 10 points for Bellarmine.
"The last moments for me, incredibly humbling," said Bellarmine coach Scott Davenport, a former assistant coach at Louisville under Denny Crum and Rick Pitino. "If you look at college basketball Division I, II and III, there are only three national champions a year. That is incredibly humbling. It's impossible to describe how difficult this is to achieve. They do not give these away."
Okesene Ale scored 17 points for BYU-Hawaii.
Davenport said tightening up the defense against Chang in the second half was key. Chang didn't get as many good looks at the basket, shooting 3 of 10 after he was 9 of 10 in the first half.
"We altered our defense to get fresh guys on him," Davenport said.
BYU-Hawaii overcame turnovers down the stretch to get within 69-68 on Heath Gameren's 3-pointer with 10.6 seconds left. The Seasiders had the ball with 2.1 seconds remaining, but Bellarmine broke up a long inbounds pass and time expired before BYU could get off a shot.
"I'm extremely proud of this group that survived all year long and worked hard and keep fighting no matter what happens," BYU-Hawaii coach Ken Wagner said. "I thought they did that today. We came up short, but I don't think it was their effort or heart or anything like that. Bellarmine played an excellent game."
Chang picked up his fourth foul with 12:32 remaining and headed to the bench with his team trailing 58-53. He was held to one field goal the final 8 minutes.