Shin recorded a 5-under total at the Ocean Course of the Half Moon Bay Golf Links and was two shots in front of Paula Creamer. Two-time defending champion Lorena Ochoa shared third place at 3-under 69.
"I think as long as you finish in the red numbers, you are in a good position not too far from the lead," said Ochoa, the world's top-ranked player, who is looking for her eighth victory of the season.
Ochoa shared third place with Annika Sorenstam, a five-time winner of this event who has said she will retire at the end of the year.
Also tied for third were Angela Stanford, Na Yeon Choi, Song-Hee Kim and LPGA Championship winner Yani Tseng.
The tournament features an elite field of 20 players.