The American fired a closing round of 65 to finish on 20-under, two shots clear of 54-hole leader Mirim Lee.
Four birdies in five holes saw Kerr take the turn in 32 and surge up the leaderboard. After notching up another birdie on the 10th Kerr chalked up a bogey on the 12th, but then reeled off four birdies on the trot to hit the front. The American blemished her card with a bogey on the final hole, but the hard work had already been done.
Lee endured something of a rollercoaster ride on the Aviara Golf Club course, opening her round with a bogey before slumping to a double-bogey six at the par four.
The South Korean recovered to produce four birdies over the remainder of the front nine, and continued that improvement as she gained a further shot at the 13th. It appeared that Lee was making a move to reclaim her lead when she eagled the 16th to draw level with Kerr at the top of the leaderboard, but it was from there that it all went horribly wrong.
First an errand tee shot at the 17th found the trees to the left of the fairway and then her recovery shot settled in the rough as Lee recorded her second double-bogey of the day, and what a costly one it would be as her round of 70 proved only enough for second.
World number one Lydia Ko came home in third place, the New Zealander finishing three shots off the pace. Ko's round of 67 continued her run of consecutive under-par rounds on the LPGA Tour, with her total now up to 28, one off Anika Sorenstam's record.
Alison Lee was next best on 16-under, with world number two Inbee Park a further shot back in fifth place.
Ilhee Lee became the third player in as many days to tie the course record, with her final round 64 equalling the mark set by Morgan Pressel in the second round and Se Ri Pak in the third round.