Ochoa, the defending champion, birdied the final hole in a four-under 68 for a 16-under total of 200, one stroke in front of South Korean Jee Young Lee and American Angela Stanford, who had held the lead after both the first and second rounds.
Stanford posted a 70 and Lee had a flawless 67 in her quest for her first victory on US soil.
"It was a good day," said Ochoa, the defending champion. "Started the day, I was in second place, and I ended up on the lead with one stroke, and I feel good.
"I had a great start today, made four birdies in the first five holes, I think, and then it was just kind of slow.
"I give myself a lot of chances to miss a few short putts and not get frustrated. And this golf course is one of those that you can shoot really low, so anything can happen. So I'm just going to be really alert and try to be aggressive and just get a low round tomorrow."
Former world number one Annika Sorenstam of Sweden, who won the season-opening SBS Open and is a three-time winner of this event, had a slightly disappointing 72.
She gave up shots at the 16th and 17th and finish seven strokes adrift on nine-under.
Ochoa and Stanford both birdied the first two holes. Ochoa added more at the fourth and fifth but dropped a shot at the 12th before her birdie at 18.
Stanford, who opened with a course-record 10-under 62 on Thursday, fell back after a couple of mid-round bogeys, but capped her round with back-to-back birdies at 17 and 18 to keep a second career victory within reach.
Stanford's only title to date came at the 2003 ShopRite LPGA Classic.
"I really just tried to stay within my own game and play my own game, and I need to do the same thing tomorrow, and I need to just keep giving myself chances and not get ahead of myself," Stanford said. "I think I kind of got ahead of myself going into 13, 14, 15. I think I started to press a little bit, and I need to just, one shot at a time, and just give myself chances."
Lee, who won the LPGA Tour's 2005 Nine Bridges Classic in her native South Korea, came close to her first victory in the United States last year when she lost to Norway's Suzann Pettersen in a playoff at the Michelob ULTRA Open.
On Saturday Lee picked up shots at the second, fourth and seventh and added birdies at the 13th and 16th as she posted her third straight 67.
South Korean Inbee Park (65) and Briton Lindsey Wright (66) were tied for fourth at 12-under 204.
Ochoa seizes lead at Safeway International LPGA