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.
The guard prospect was one of the top players at the annual Spiece Run N Slam event.
SMU has signed a second player from Australia, 6-foot-11 forward Harry Froling, to a national letter of intent. The Mustangs previously signed guard Tom Wilson from Australia.
There's nothing to suggest the Jayhawks won't end up atop the Big 12 for a 13th season in a row. But what about a return to the Final Four?