Walter Morgan and CBS golf analyst Gary McCord share third place at 4-under-par.
Saturday, under much more benign conditions, the stroke average fell almost two strokes. Thirty-five players posted rounds of par or better on Saturday, while only 11 did so in the first round.
Dougherty opened with a five-foot birdie at the first but it was his play around the turn that caused his name to be at the top of the leaderboard. He dropped in two birdies at five and six but his approach shot at the par-5 eighth separated him from the field.
He roped a 5-wood to four feet at No. 8 to post an eagle and grab a two-shot lead. Dougherty closed out the front nine with a five-foot birdie on nine for a 6-under 30.
Dougherty ran into a bit of trouble at the 10th when he three-putted for bogey, but he rebounded with a 15-foot birdie putt at 11 to reclaim the lost stoke.
The 54-year-old cruised along with pars, including a clutch save at the 15th after a poor drive left him the trees. But he ran home a four-foot birdie at 16 to get two ahead of Fleisher.
'I'm thrilled and lucky to play a good round like this on as a good a course as this is,' said Dougherty. 'Making the putt on the first hole gave me confidence and I had a great front nine today.'
The last time Dougherty owned the 36-hole lead in a tournament was last May in the TD Waterhouse Championships. He went on to win the event by eight shots.
'I'll just try to do what I can tomorrow and see where the cards fall,' said Dougherty, who won once on the PGA Tour. 'It would be a thrill to win here.'
Fleisher got close to Dougherty after a 30-foot birdie at the 13th but he dropped a shot at No. 14 when his approach came up short of the green and he failed to hole a six-foot save. He closed with a three-foot birdie at 15 and a 10-footer at 16 to shoot a 66 and take sole possession of second.
'The conditions were a lot easier today,' said Fleisher, who owns three top-five finishes in four starts this season. 'I made some putts today but I'm not striking the ball particularly well. It will be a shooting match.'
Bruce Lietzke (66) and Hugh Baiocchi (68) share fifth place at 3-under-par 141.
Overnight leader Dana Quigley struggled to a 1-over 73 on Saturday and is tied for seventh with Jack Spradlin and Hale Irwin, who posted second-round 69s.
Full-field scores from the Audi Senior Classic