However, Australian Scott rebounded with a birdie at the par-three 17th before parring the last to card 66 in blustery conditions for a nine-under total of 201.
"I was trying to get a ball dry for a start and eventually did on my fifth (shot)," the former world number one told Golf Channel about his struggles at the par-three 15th.
"That's what this course is all about. It's going to reward really great shots and severely punish ones that are just off, especially as you come around that Bear Trap," he said of the infamous three-hole stretch from 15 to 17.
"It got me today so hopefully that's out of the way and I can do a little better tomorrow."
Overall, Scott was delighted with his form, having piled up seven birdies in the first 13 holes on a tricky course where only 21 players in the field of 77 shot under par during the round.
"I am playing great and the way I played today was beautiful," said the 2013 Masters champion. "I hit a bad shot, my first shot on 15, and the wrong spot to do it. I just had to get back on it, and I did."
Scott's playing competitor Garcia, bidding for a ninth PGA Tour win, sank a six-foot birdie putt at the par-five 18th to shoot 67 and join the Australian at the top of the leaderboard, four shots clear of third place.
"They were playing tough today," Garcia said of the closing holes at PGA National where he finished up par-par-bogey-birdie.
"The main thing you do is you try to commit to the shot you want to hit. I was happy the way I played them, a little bit conservative but very good."
Blayne Barber (69), a rookie on the PGA Tour last season, was in third place at five under, with fellow Americans Justin Thomas (68) and second-round leader Rickie Fowler (74) a further stroke back.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Andrew Both)
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