The Dons (11-13, 4-7 West Coast) shot 57 percent from the floor, including 72 percent after halftime, and were 14 of 23 from 3-point range -- 9 of 10 in the second half.
BYU led 48-39 at halftime and 62-47 after Matt Carlino's jumper with 14:25 to play, but San Francisco came alive after that, outscoring the Cougars 52-25 the rest of the way. Holmes' 3-pointer with 5:56 left put the Dons ahead for good, 75-72, and San Francisco went on to lead by as many as 16.
With the win, San Francisco avenged January's 80-76 home loss to BYU.
Mike Brey is looking at former Notre Dame players to fill two assistant jobs that have opened up with the departures of Martin Ingelsby and Anthony Solomon.
Purdue's 2016-17 prospects got a jolt Wednesday when forward Caleb Swanigan announced he will return for his sophomore season.
Clemson's Jaron Blossomgame says he is withdrawing from the NBA draft and returning to school for a final season.