Watson made 14 of 16 free throws overall and finished with a career-high 27 points while Derksen had 11 points and a career-best 13 rebounds. Chase Foster added 13 points for San Francisco (3-1).
Malik Thames hit a 3 to extend UC Riverside's lead to 57-52 with 58 seconds left.
Watson hit the first two of three free throws but Dont'e Reynolds grabbed the offensive rebound on the third. Watson was fouled again and hit both free throws, cutting San Francisco's deficit to one, 57-56, with 38 second to go.
Secean Johnson was called for an offensive foul on the other end before Watson hit a streaking Derksen for the winner.
Riverside's Steven Jones missed a running heave from a couple steps inside half court as time expired.
Thames led the Highlanders with 15 points, all on 3s.