That double bogey closed a round of 5-under 67 on the TPC at Sugarloaf. Mickelson completed 54 holes at 21-under-par 195.
After tying the 18-hole record with his 63 in the first round, Mickelson set a new 36-hole record with his 128 total. That was one better than Larry Nelson was in 1988.
The defending PGA champion leads after three rounds for the 19th time in his PGA Tour career. Lefty has gone on to win 13 of the first 18 of those events.
'He can be beaten. This week, I'm not so sure. It would have be nice if he prepared for Augusta at Augusta rather than here,' joked Zach Johnson. 'I'm going to say the odds are against us. He's a steam train right now and we're just trying to hop on board.'
Johnson fired the low round of the day as he shot 8-under 64 to get to 13-under-par 203. He was joined in second place by Jonathan Byrd, who birdied six straight holes on the back nine en route to a 6-under 66.
Two-time Masters champion Jose Maria Olazabal is alone in fourth at minus-12 after a 69. Doug Barron, Steve Flesch and J.J. Henry share fifth at 10-under-par 206.
Mickelson, who has won here twice and both times the event was weather- shortened, parred his first two holes. He then caught fire to really distance himself from the field.
The 35-year-old former Arizona State star made a 10-footer for birdie on three. Mickelson's approach at the fourth spun right past the cup setting up his 8-foot birdie putt.
Mickelson poured in a 20-footer for birdie at the fifth, then got up and down for birdie from a bunker on six. After sinking another 20-foot birdie putt on the seventh, Mickelson was 11 clear of the field at 21 under.
The 2004 Masters champion three-putted for bogey on the eighth, then came right back with a birdie on nine from 15 feet out.
Despite a two-putt par on the par-5 10th, Mickelson had played the first 46 holes of the event with 23 birdies, 21 pars and two bogeys. Lefty stuck his approach within 3 feet at 11th. That birdie got him to 22 under and was his 37th straight green hit in regulation.
The run ended when Mickelson missed the green on the par-3 12th, but he made par from the fringe. He dropped in back-to-back birdies from the 13th to move to 24 under. His birdie on 14 gave him the tournament record of 26 birdies.
Mickelson stumbled down the stretch. He missed the green left on the par-3 16th and could not get up and down for par. At the last, his second shot came up short and in the water.
After a drop, Mickelson's fourth also found the water. He finally reached the green in six and drained a 26-footer for double bogey as his lead fell to eight from a high of 12.
'I played well. It was fun to hit shots and have them end up where I wanted them to and end up making the putts,' Mickelson said. 'It was a fun first three rounds. I came out a little early today, about three-and-a-half hours before I played and I got a little bit tired and I hit some sloppy shots there at the end. Tomorrow I'll probably not come out quite so early. '
Johnson birdied four straight holes from the third. Around the turn, he birdied four of six holes from the 10th. After a bogey on 16, Johnson birdied the last to end at minus-13.
'You have to go out there and make birdies,' said Johnson. 'Phil is playing extremely good golf. I feel like I'm playing decent as well. Today I had a great round.'
Byrd was even par through his first 11 holes with a birdie and a bogey. He poured in six consecutive birdies from the 12th, including a chip-in birdie on 17, share second.
Retief Goosen is alone in eighth place at 8-under-par 208 after a 69. Alex Cejka, Charles Warren, Mark Wilson, Briny Baird, Rich Beem, Todd Fischer and David Howell are one stroke further back at minus-7.