Searching for his maiden win on the Tour, Mallinger was flawless with a course-record equaling nine-under 62, remaining bogey-free through the opening two rounds to reach 14-under 128 at CordeValle Golf Club.
The 33-year-old pulled away from the leading pack when he knocked in an 11-foot putt for eagle on the 15th hole and then stepped on the gas with birdies on the 17th and 18th.
Venezuela's Jhonattan Vegas (67) and American Billy Horschel (65) finished the day tied for second at 10-under.
Australian overnight leader Nick O'Hern couldn't maintain his course record tying rage from the opening day, backing up his 62 with an even par 71 to share fourth place with Belgian Ryder Cup rookie Nicolas Colsaerts (68) and American Scott Dunlap (63) at nine-under.
Mallinger was in jovial spirits after the round, joking with reporters not to talk about his bogey-free streak so as not to jinx his form.
He did however open up about his blistering day when asked how often he felt this good during a round.
"It's only the second time I've shot 62 in seven years out here, so it's not very often," he said.
"It's just one of those days where everything just kind of clicks and you just roll with it. I drove it great, irons were great, and made putts."
The California native was extra comfortable on the greens. "It's the same grass I practice on at home," Mallinger, who resides in Long Beach, said.
"I'm just real comfortable with the speed. I just have some good thoughts over the putter right now, and that's not every week.
"Hopefully I can take advantage of it and keep it going into the weekend."
After finishing second at the Humana Challenge back in January, Mallinger believes he can go one further on the weekend.
"It's difficult. I've been out here six years and I haven't won yet. Been close a lot of times, lost in a playoff, had a bunch of third places," he said.
"I feel like I'm close. I don't think I would be up here if I wasn't. I'm not going to go into the weekend scared.
"I'm going to play as hard as I can and compete as hard as I can."
- Sports & Recreation