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.
White House officials said Tuesday that the Villanova men's basketball team will visit with President Barack Obama next week.
Kendrick Nunn, who pleaded guilty to misdemeanor domestic battery last week, has been dismissed from the Illinois basketball team.
Delaware has hired Notre Dame assistant Martin Ingelsby as its next men's basketball head coach, sources told ESPN's Jeff Borzello.