Dougherty cooled off considerably after his scorching five-hole start. He parred nine straight holes before birdieing the 15th and 17th. At the par-4 finishing hole, Dougherty recorded his first bogey of the week when he missed the green with his approach shot.
Doughertys Day-Two 6-under-par 66 leaves him at 16-under for the tournament; five shots clear of defending champion Dana Quigley and Hugh Baiocchi.
Quigley kept alive his opportunity to repeat by shooting 68 on Saturday, while Baiocchi shot 67.
Ted Goin, the rookie who started the day two off the lead, carded an even-par 72 to remain at 8-under-par, six back of Dougherty.
Dougherty is seeking his first victory of the season after a pair of third place finishes. He captured last years Coldwell Banker Burnet Classic.
Full-field scores from the TD Waterhouse Championship