Mallinger finished the day at 15-under-par 198 at CordeValle Golf Club, two shots better than Jonas Blixt.
The Swede charged into second place, draining five birdies over the last eight holes to card a 5-under 66 and finish at minus-13.
Sharing third place at 12-under 201 after 54 holes were Charles Howell III (66) and Jason Kokrak (67).
Alexandre Rocha and Vijay Singh each registered 66s Saturday to move into a tie for fifth at minus-11.
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