Tim Clark and Chris Anderson finished three shots back at 9-under-par 135.
Huston, who was part of a three-way tie for the lead after the opening round, played the back nine first at Annandale Golf Club and hit a pitching-wedge to eight feet for a birdie at the par-5 11th.
The 42-year-old hit an 8-iron off the tee at the par-3 15th to 12 feet and ran home the putt for a birdie. Huston then dropped his approach inside five feet for a birdie at the 17th to make the turn at 9-under.
'Much calmer earlier today,' said Huston, a six-time champion on the PGA Tour.
Huston continued his fine play on the front side and reached the green in two at the par-5 fifth en route to a birdie.
Huston followed that up with a birdie at the par-5 seventh and knocked a 7-iron within five feet of the cup at the par-3 eighth. Huston drained the short birdie try to pad his advantage heading into the weekend.
'Better today. No bogeys,' said Huston. 'I did miss a couple short birdie putts. Everything is clicking well.'
Defending champion Luke Donald, who earned his first career victory on the PGA Tour at this event last year, finished alongside Shigeki Maruyama and Paul Stankowski at 8-under-par 136.
Stankowski tallied a bogey and a birdie over his first nine holes but a strong back nine moved the 33-year-old into contention.
He picked up a birdie at the 10th and ran off back-to-back birdies starting at the par-3 12th. Stankowski then hit a 3-iron to 12 feet at the par-5 last and settled for a closing birdie.
'A little less windy today,' said Stankowski. 'Great course. The greens are soft but have speed.'
Corey Pavin, David Frost, Willie Wood, Jim McGovern and Brett Quigley tied for eighth place at 7-under-par 137.
Kent Jones, Woody Austin, Jose Coceres, Carlos Franco, Paul Gow and John E. Morgan were one shot further back at 6-under-par 138.
The 36-hole cut fell at 1-under-par 143 with 71 players qualifying for the weekend.
Among those who failed to make the grade were Notah Begay III, Matt Kuchar, Craig Perks and John Daly.