Watson was 7 of 12 from the floor as San Francisco (9-11, 3-5 West Coast) shot 53 percent from the floor. Tim Derksen had 15 points and eight rebounds, Kruize Pinkins scored 12 and Mark Tollefsen contributed 11 points.
Pepperdine's Stacy Davis made a pair of free throws to tie it at 28 with 24 seconds left in the first, but Chris Adams drilled a 3-pointer with seven ticks left to put San Francisco up 31-28 at the break.
The Dons opened the second half on a 19-6 run to open a 50-34 lead and cruised to the win.
Davis led Pepperdine (12-7, 5-3) with 23 points and Shawn Olden added 15 points. The Waves were just 2 of 13 from beyond the arc.