Daniel Chopra, Jeff Klauk and Bob Friend finished tied for second at 4-under-par 136.
Williamson got off to a tough start with a bogey at his first hole, the par-4 10th, but he countered with a birdie at the 17th to make the turn at minus-2 for the tournament.
The 30-year-old picked up another birdie at the first before his second bogey of the day at the par-4 third. Williamson persisted, however, and got the shot back with a birdie at the very next hole.
At the par-4 sixth, Williamson hit a 3-iron to four feet and rolled home the birdie putt to reach 4-under.
'That might have been the best shot I've hit all year,' said Williamson, whose only top-10 finish this season was a tie for third at the Lake Erie Charity Classic in June. 'The wind was blowing left to right. I visualized it in there and executed it perfectly. It was kind of gratifying.'
Williamson took the outright lead with a birdie at the following hole. The California native was content with his round but in awe of the newly renovated Crestview Country Club layout.
'I think that's a 9-under for me,' said Williamson. 'I've missed some greens but I've had a lot of fringes. You've got 10 scoring holes where you can make birdie but the other eight are par-bogey holes if you don't pay attention.'
Brian Sharp fired a 5-under 65 to finish two shots off the pace at 3-under-par 137 alongside Mike Brisky, Jeff Freeman, Nolan Henke, Andy Sanders and Ahmad Bateman.
First-round leader Barry Cheesman struggled with a round of 73 that included one double-bogey and five bogeys. He finished at 2-under 138.
Casey Martin, one shot behind Cheesman after the opening 18 holes, carded a 4-over 74 to slip back into a tie for 33rd at even-par 140.
The halfway cut fell at 2-over-par 142 with 67 players qualifying for the weekend. Among those who failed to make the cut was defending champion Jason Dufner.
Full-field scores form Wichita Open