Blixt finished at 16-under-par 268 -- one stroke better than Jason Kokrak and Tim Petrovic.
The Swede birdied the par-4 17th, moving to minus-16 at CordeValle Golf Club.
Kokrak pulled to within a stroke when he eagled the same hole, but parred the last to register a round of 68, finishing one back at 15-under.
Petrovic, meanwhile, had a chance to force a playoff but two-putted for par on the 18th, also ending a single shot off the pace.
Jimmy Walker zoomed into a share of fourth place at minus-14 thanks to a course-record tying 9-under 62.