Rose had six birdies and an eagle on another pristine day along the Pacific, and he stretched his lead to six shots at one point along the back nine of the South course.
But, double-bogeys on the par-four fourth and 14th holes and a bogey on the par-five 18th hole tarnished his scorecard, though Rose still ended the day in pole position.
Former world No.1 Scott stunned the crowd with a 200m second shot he fired into the par-five 17th (his eighth hole) for a tap-in eagle, which highlighted a 66 that gave him an eight-under total and a share of ninth. "If you take into account the town and the vibe around Torrey Pines, this is my favourite golf course and golf tournament".
"I always pride myself on the golf courses I've been able to win on, and this one is another great course with a lot of history", Rose said.
"Sixty-five around the south course, I don't care what the conditions are, it's a good score".
Tiger Woods, meanwhile, produced a one-under-par 71 as the seven-time victor stalled on the weekend.
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Woods made a relatively quiet return for his first official event since he captured his 80th PGA Tour victory at the Tour Championship in September. He shot another 70 on the North, which was about two shots easier than the South, and was 11 shots behind.
Woods enjoyed a return to form last year, the 14-time major victor ending his five-year wait for a title by claiming the Tour Championship, having impressed at The Open and US PGA Championship.
"I'm playing well and just need to keep producing", said Rose, whose 20 birdies this week are the most in the field.
"When you go South on the first day you are trying to survive", said Rahm, who was started on the 10th and turned with a seven-under 29 before following his only dropped shot of the day at the third with four birdies in a row from the fifth.
"I got a little bit sharper each day and my rounds got a little bit cleaner, I made less mistakes", said Woods. Didn't know if I could make it to Florida, first of all. "By the time I got it sorted out, it was a bit too late".
It was never going to be enough to catch Justin Rose, though Woods believes he got enough out of the week to feel reasonably well about the start of his year.