American Mallinger repeated the feat of Nick O'Hern, hitting a nine-under 62, to head the field by four as the Australian slipped down the leaderboard.
Like O'Hern on day one, Mallinger was bogey-free for his round - indeed, he is without a blemish on his card so far this week - but he also threw in an eagle at the par-five 15th to go with seven birdies, putting him 14 under overall.
That equated to a four-shot lead over compatriot Billy Horschel and Venezuela's Jhonattan Vegas.
O'Hern could only manage a level-par 71, putting him in a share of fourth on nine under alongside Belgian Ryder Cup star Nicolas Colsaerts and Scott Dunlap of the United States.
Dunlap was eight under, with seven of his eight birdies coming on the back nine as he came home in 29.
England's Greg Owen led the British challenge as his two-under round put him seven under overall and in a tie for ninth, three strokes ahead of Scotland's Russell Knox and American defending champion Bryce Molder.
Another Englishman, Brian Davis, scraped into weekend play on one under, making the cut with nothing to spare, but Gary Christian bowed out at the halfway stage.