The somewhat deflating finish left Potter, whose lone PGA Tour victory was in 2012, locked with fellow American Johnson at 14-under 201, two strokes clear of Australian Jason Day and American Troy Merritt.
"It's just a truly unbelievable thing to win here at Pebble", said Potter, who moves to a career-high of world No 73.
It gave him two-under-par 70 and a share of second alongside world No.1 Dustin Johnson (72), five-time major victor Phil Mickelson (67) and Chez Reavie (68). Potter chipped in for birdie behind the seventh green.
After a 2017 which was below his own lofty standards, the Queenslander looks in a mood to climb back to the top of the golf world and with four events of the season gone is yet to finish worse than T11.
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"He's waving his putter like Harry Potter's wand", quipped Riley as the boy wizard's golfing namesake saw off the challenge of world No1 Dustin Johnson to win by three shots in California.
Scott dropped outside the top 50 for the first time in 413 weeks, since April of 2010. "I knew I had probably a two-shot lead, but you never know what could happen out there". The hole cost Reavie his chance of glory when he recorded a bogey six there and Phil Mickelson, who played an exquisite chip shot from the rough for his third stroke, was the only man in-contention to birdie the hole.
He wound up winning by three shots over Johnson (72), Mickelson (67), Day (70) and Chez Reavie (68).
Plus, because of 25 pro-am teams making the cut to play Sunday, the draw can get a little out of whack.
Up-and-coming Englishman Ben Taylor's maiden win on the Web.com Tour, at the Club Colombia Championship, was a great step for him and brought back some fond memories for me. He made eight pars and a bogey on the back nine, with most of the damage coming on a wedge that came up short and into the bunker on the par-5 14th.
Ultimately, Potter simply outplayed him.
There is nothing fancy about Potter's game or how he won for the second time in his career. Day was coming off a win at his last start and is a perennial contender at Pebble.
He was the one chatting with Clint Eastwood and posing with the crystal trophy that comes with a $1,332,000 check and a return to the Masters. I hope Potter goes on to have more but even if he doesn't he will always have this.
Reavie, a playoff loser in Phoenix last week, went out in 31 and was at 15 under, two shots behind.