A day after equalling the CordeValle course record with a nine-under 62, he could manage just a 70 for 15-under-par total as his four-stroke lead was cut in half by Sweden's Jonas Blixt.
Having not had a single bogey on the first two days, Mallinger carded two on the front nine today against one birdie.
But he picked up a further two strokes on the back nine to ensure he at least stayed atop the leaderboard.
"I just didn't have it all," Mallinger told www.pgatour.com. "I didn't drive it as well as I did yesterday.
"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 the lead, still got a good spot, and look forward to tomorrow."
Blixt carded a five-under 66 to put the pressure on Mallinger, but it did not look like being that way when he was one over through eight.
He hit six birdies in his last 10 holes, though, to sit 13 under overall.
One shot behind him on 12 under were Americans Charles Howell and Jason Kokrak, after rounds of five under and four under respectively, while Fiji's Vijay Singh and Alexandre Rocha of Brazil both hit 66s for a share of fifth on 11 under.
Scotland's Russell Knox made a charge with a bogey-free six-under round to lie in a share of seventh on 10 under, where he was joined by, among others, England's Greg Owen and New Zealand's Danny Lee.
Defending champion Bryce Molder was in joint 12th on nine under, as were Ryder Cup star Nicolas Colsaerts and Australia's Nick O'Hern who, after carding a 62 on the opening day has not picked up another stroke.