Miles finished with 13 points for the Toreros (9-8, 2-0 West Coast), who snapped a six-game losing streak against San Francisco. Chris Anderson added 10 points and five assists.
San Diego hit 11 of 22 3-pointers, with most coming at key moments.
Two straight 3s by John Sinis started a 9-0 run that put the Toreros ahead 26-17. After San Diego took a 46-32 halftime lead, the Dons opened the second half on a 20-7 run to get within 53-52 on a 3-pointer by Derksen with 12:14 remaining.
Miles responded with back-to-back 3s for San Diego to build the lead back to seven, and the Toreros held on from there.
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.