Scheffler shot a bogey-free, eight-under-par round of 64 to share top spot on the leaderboard at 11-under with Belgian Thomas Detry and Sweden's Ludvig Aberg.
The American sank a 35-footer to make birdie on the par-3 17th and then followed up with an aggressive approach on the par-5 18th.
"Boring is always nice on the card, keeping a clean card is good," said Scheffler of his avoidance of bogeys on the historic Californian course.
"I felt like I didn't have to struggle for many pars. I kept the golf course in front of me, made some nice puts and hit some quality shots into the greens. I just gave myself a lot of opportunities," he said.
"I did not realise how much it rained overnight. It was really wet. So like on a lot of these back-to-front greens it's a big adjustment going from hitting a pitching wedge to hitting an 8-iron to try to take off spin," he added.
The soft, wet course encouraged players to attack the greens and Aberg certainly took that approach, following up a birdie on the first with an eagle on the par-5 second.
After a thumping 302-yard drive, the 24-year-old landed his approach 35 feet from the hole and sank his putt superbly.
Aberg was outstanding on the greens as he reached the turn on five-under and he added two more birdies on the back nine on the 11th and 14th.
"Obviously got off to a nice start with a couple of long putts, I don't remember the last time I did that, so obviously that's a little bonus. I felt like I kept playing quite well and kept being disciplined, so it was nice," said the Swede.
Aberg, who played college golf in the USA for Texas Tech and turned pro in June, picked up his first win on the PGA Tour in November at the RSM Classic, following up his win on the DP World Tour in Switzerland in September.
That month he grabbed global attention with his excellent performance in Europe's Ryder Cup win over the United States in Italy.
Building on experience
Aberg said he would draw on those experiences as he searches for his second PGA Tour victory.
"I think any time that you get to win a tournament and feel those emotions coming on the last couple holes and being in the lead and trying to chase down the lead, there's always a lot that you can learn from that," he said.
"I don't try to get too high, not too low, and obviously the experiences that I had last year was a lot of good ones, try to keep building on that and see where that takes us over the weekend."
Overnight leader Detry teed off on 10 and was three-under at the turn but was undone by bogeys on the fourth and fifth as he carded a two-under 70.
"I know my game is really solid, I've been playing some really good golf now for the last couple years, so all I have to do is really trust it and keep building on all these good rounds that I've done under pressure," said the Belgian, who challenged last week at Torrey Pines before a disappointing final two rounds.
Patrick Cantlay recovered from driving out of bounds on the 18th to make par and finish a stroke behind the leading trio after his two-under 70.
American Justin Thomas, who shot a five-under 67, Argentine Emiliano Grillo and France's Matthieu Pavon - coming off his historic victory at Torrey Pines on Sunday - were all two shots off the lead.
