The 33-year-old Mallinger had a 15-under 198 total at CordeValle after opening with a 66 and matching the course record with a 62 on Friday.
"I just didn't have it all. I didn't drive it as well as I did yesterday," Mallinger said. "I think I hit every fairway yesterday, and then today I just got off to a weird start. But I hung around there and made some birdies on the back nine that got me back into position. Still got lead, still got a good spot, and look forward to tomorrow."
He has finished second twice in his seven-year career on the tour, losing in a playoff to Bo Van Pelt in Milwaukee in 2009. Mallinger had the third-round lead for the second time in his career. He shared the lead at the 2009 Byron Nelson Championship and ended up tying for sixth.
"I'm going to still stay aggressive and try to make as many birdies as possible," Mallinger said. "It's going to be a birdie day. I mean, it's supposed to be nice tomorrow."
Sweden's Jonas Blixt was second after a 66. He birdied five of the last eight holes.
"The front nine is a little harder," said Blixt, coming off a third-place finish last week in Las Vegas. "The back nine you can make a couple birdies. Hopefully, I can finish like I did today.
He had a simple game plan for Sunday.
"Make birdies," Blixt said.
Charles Howell III and Jason Kokrak were 12 under. Howell had a 66, and Kokrak shot 67.
"It'll be a shootout tomorrow," Howell said. "The greens are so soft and there will be a lot of birdies, but at least I have a chance."
He won the last of two tour titles in 2007.
Kokrak is in his first year on the tour after winning twice late last year on the Web.com Tour.
"This is the first time I put myself in really good position," Kokrak said. "I just want to go out tomorrow and do the same things I did today."
At 167th on the money list, he's in danger of losing his tour card.
Vijay Singh and Brazil's Alexandre Rocha were 11 under. They shot 66.
The 49-year-old Singh won the last of his 34 PGA Tour titles in 2008. He birdied Nos. 15 and 16, eagled the short par-4 17th and closed with a par.
"I found something in my putting that's working really, really good, so hopefully tomorrow I can get some going," Singh said. "I've changed my grip a little bit and it's flowing really freely. So that's a big plus."
British Open champion Ernie Els was 5 under after a 69.