Shin, still looking for her first tour win after her best finish this year, had a 68 to finish two shots behind.
"They were fearless," Shin said about her playing partners, "They just went for it."
Playing together for the fourth straight day, neither Ko nor Lewis hit any dazzling shots early. Ko's second of three bogeys came on the 417-yard, par-4 seventh in which her tee shot hit a tree and dropped in the rough. Lewis' 10-foot birdie putt on No. 9 lipped out.
Ko pulled into a first-place tie at 10 under as they made the turn on a picture-perfect spring day, then took the lead with a birdie on No. 13. Lewis went in the bunker, missed the green and two-putted for bogey to fall two back.
"The front nine, I did everything I wanted to do, the putts just didn't go in," Lewis said. "I expected her to do exactly what she did today. ... She hit every shot she needed to make from 13 on in."
There were two holes-in-one Sunday: Jimin Kang on the 164-yard third and Dewi Claire Schreefel with a 7-iron on the 157-yard 12th hole that earned her a $100,000 prize from China Trust Bank.
The weather held for the final day after fog and rain delays earlier in the tournament.
This event was the LPGA's first in the Bay Area since the 2010 CVS/pharmacy LPGA Challenge at Blackhawk in Danville.
Organizers and club officials are optimistic about keeping the tournament at Lake Merced.
Donna Lowe, Lake Merced general manager, hopes an announcement would come within a month to begin planning for 2015.
San Francisco Mayor Ed Lee has spoken with Swinging Skirts Chairman Johnson Wang, while Lowe has received positive feedback from LPGA Commissioner Michael Whan, players and their caddies.
"So far, it's just been amazing and very positive and uplifting," Lowe said of the feedback.
DIVOTS: Michelle Wie, who won last week in her home state of Hawaii, tied for ninth at 2 under. Second-ranked Suzann Pettersen shot a 70 to finish at 3 over in her first event since last month after missing three tournaments with a back injury. Top-ranked Inbee Park tied for fourth at 6 under.