In all he notched five birdies on the day and finished with a 54-hole total of four-under 209.
That was six shots off the clubhouse lead when he walked off the par-71 CordeValle course.
Woods capped his round with a birdie at the par-five ninth, but regretted that he couldn't make more of good scoring conditions.
"The golf course could have been had today,'' he said.
Woods, winner of 14 major titles, hasn't won a tournament since 2009.
His equal fourth place at the Masters in April was his best result so far this season, and he suffered knee and tendon injuries at Augusta and played sparingly since.
He withdrew hurt from the first round of the Players Championship in May and finished tied for 37th at the WGC Bridgestone Invitational in August.
He missed the cut at the PGA Championship, his last prior US tour start.
After this week, Woods is due to have another month off before heading to Australia for the Australian Open and the Presidents Cup, where he will play as a captain's pick by Fred Couples in the matchplay showdown between the United States and an international team.
- AAP