The American former world number one completed his third round in 69 to sit 14 under par for the tournament, four shots ahead of Canada's Brad Fritsch, who went round in 70.
The pair were due to start their final rounds right away, and much of the field were already under way with theirs, after fog caused havoc at the Torrey Pines course Saturday.
Brandt Snedeker had joined Fritsch on 10 under overall after going through the first six holes of his final round in three under.
England's Ross Fisher was the highest-placed European in the field on six under.
He finished his third round in 73 and had yet to start his fourth.