After the field played 36-holes on Monday, Stanford held just a one-shot lead over the Waves heading into the final round. Pepperdine dogged the Cardinal all afternoon and made up the shot it needed to earn a share of the team title at 17-over 869.
It marks the Waves' fourth win of the season and second this spring following their victory at the Anuenue Spring Break Classic in Maui.
Perhaps the biggest surprise of the Silicon Valley Showcase was Stanford's Rose Zhang didn't win it.
In her first tournament appearance since winning the Augusta National Women's Amateur two weeks ago, the world's top women's amateur finished fifth at 4-over par 217 following rounds of 70-74-73 in windy conditions.
Pepperdine's Lion Higo, a junior from Gold Coast Australia, shot a final round 73 to overtake 36-hole leader Sadie Englemann of Stanford to claim the individual title at 1-over 214. It's Higo's second win of the season following her maiden victory at the Golfweek Red Sky Classic in September.
Englemann tied for second with teammate Kelly Xu, whose title hopes were dashed by a double bogey on the final hole.
Stanford and Pepperdine will now turn their attention to their conference championships, which get underway next week.