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.
College basketball fans should be excited about next season's Jimmy V Classic, an event that will feature Duke's heralded freshman class.
Jeff Goodman logs all the coaching changes following the 2015-16 college basketball season.
Can Josh Pastner keep top talent in Georgia? Will Tubby Smith change his recruiting philosophy at Memphis? New coaches face some difficult questions.