Having lined up a 25-footer at the par-four ninth, his final hole in the opening round at the TPC Scottsdale, Mickelson watched in anguish as his ball caught the right edge of the cup before rolling around the back of hole and spinning out.
"The last six feet it was right on glide slope, it should have been right in the middle," Mickelson told Golf Channel after shooting an 11-under-60. "To have that putt on line, I am kind of mortified that it didn't go in."
The four-times Major champion, who had pointed his putter in the direction of the ball as it headed towards the cup, clutched his drooping head with his left hand when his hopes of a 59 were so cruelly dashed.
Mickelson had to settle for a share of the course record at the TPC Scottsdale - which he already held jointly with Grant Waite and Mark Calcavecchia - but grabbed a commanding four-shot lead in the fifth US PGA Tour event of the season.
Thirty-three players were still out on the course when play was suspended for the day in fading light after the start of the opening round had been delayed for an hour due to morning frost.
Americans Brandt Snedeker, Ryan Palmer, Jeff Maggert and Ted Potter Jr, along with triple Major winner Padraig Harrington of Ireland in his first start of the year on the US circuit, opened with 64s.
Belgian rookie Nicolas Colsaerts and American Brian Gay, winner of the Humana Challenge at La Quinta 11 days ago, were among a group of nine players knotted on 65.
Masters champion Bubba Watson, who has not played since the season-opening Hyundai Tournament of Champions in Hawaii because of flu, opened with a five-birdie 67 on a near-perfect day for scoring in the Arizona desert.
"I'm ecstatic to shoot 60," Mickelson said after piling up 11 birdies with a flawless display of golf in dazzling sunshine.
"I am excited and so forth but you don't get chances to shoot 59 very often.
"I could not envision what side of the hole it would have missed on when it was a foot out. But I made a ton of putts today, I hit a lot of great shots and I drove it very well."
Winner here in 1996 and 2005, Mickelson birdied seven of his first nine holes to reach the turn in a blistering 29 amid intensifying thoughts of a possible 59.
"I was thinking 59 back on my 10th hole," said the 42-year-old fan favourite, who studied at the nearby Arizona State University. "When I had that front nine, I was thinking of it the whole time."
Mickelson, a 40-times champion on the US PGA Tour, picked up further shots at the first, third, fourth and seventh before his birdie attempt on the ninth green stunningly failed to fall into the cup.
"I am walking after it and somehow it moves at the end low and caught the lip," Mickelson said. "And even at that pace, I think it's going to lip in. That one - that was heartbreaking."
Harrington, playing in the Phoenix Open for the first time, was delighted with his seven-birdie 64.
"It's a nice score, obviously," the 41-year-old Dubliner said after hitting 14 of 18 greens in regulation. "It's a little bit behind Phil but still a nice score in itself.
"I pretty much got the most out of the round for the first 15 holes and then had three chances the last three holes and didn't hole the putts. But overall I've got a good feeling about it."
The five players who have shot 59s on the US PGA Tour are Americans Al Geiberger (1977 Memphis Classic), Chip Beck (1991 Las Vegas Invitational), David Duval (1999 Bob Hope Classic) and Paul Goydos (2010 John Deere Classic) as well as Australian Stuart Appleby (2010 Greenbrier Classic).