The 35-year-old Scot, who had started out in a share of second spot in California, admitted he’d been “left on edge all day” after being hit with a one-shot penalty early in the closing circuit.
As he addressed his ball in the middle of the first fairway, Knox saw it move and immediately called in a rules official to run him through what had happened.
Due to the ball having moved whilst the club had been off the ground, the rules official determined that there was no penalty.
Playing in the penultimate group, Knox proceeded to par the hole before picking up birdies at the second and third as he stepped up his bid to land a third PGA Tour triumph.
He’d just seen a short putt for another birdie horse-shoe out the fourth when he was approached again by a rules official walking off the fifth tee to be told that the matter had been re-assessed.
It had been deemed that he had likely caused the ball to move and, therefore, was penalised under Rule 9.4(b).
The call, which came a day after American Maverick McNealy had also been penalised under the same rule on the fifth hole, appeared to take the wind out of Knox’s sails.
He battled away bravely, finishing birdie-birdie to end up tied for seventh, but a combination of the penalty and a bogey at the fifth effectively knocked him out of the title hunt as American Daniel Berger went on to claim victory.
“It's just one of those horrible rules which every one of us is against,” said Knox afterwards. “At first, the ruling was that I didn't cause it to move, because it was such a grey area there, and, ultimately, we got it right and I did address the ball. I should have been penalised.
“Obviously it's a rule which I wish they would eliminate because obviously it happened to Maverick McNealy yesterday, no advantage, and me, obviously, no advantage today and we get penalised for it.
“It just kind of got me on edge all day, to be honest, starting that way. On No. 5 I got told they looked at it and I had to add a shot and right after a full horseshoe and facing a downhill dead bunker shot. So it was like a triple whammy on No. 5.
“Sadly, it was like the worst timing ever. I went from three-under to even in about 30 seconds, so it was, that was tough. I mean, you got to take it on the chin. I battled away after that and proud of my finish.”
Knox closed with a 70 for a 13-under total, finishing five shots behind Berger as he signed off with an eagle to claim a two-shot success.
“The first three days is the best I’ve hit the ball in many years, so that’s comforting” said Knox. “Maybe at times today I was a little sketchy, but it's Sunday, it's tough. The putter was fine, too. So it's only positives this week.”