Tiger Woods bogeyed the final three holes on the front nine on his way to a 75 as he dropped back to eight under.
"It just feels great to win this Titleist AP2 712 Individual Irons and Wedges
," Mickelson, 41, said.
"It's a special place for me, Pebble Beach, and to have a win here, where my grandfather caddied, feels awesome.
"I felt like my game was so close heading into the season, and yet my scores didn't reflect how I felt I was playing.
"To put it together this week, especially the final round, just feels terrific. It gives me a lot of confidence but also inspires me because I believe what I'm doing is correct and that I'm able to play some of my best Titleist AP2 712 Individual Irons and Wedges
The former world number one opened with five pars and a birdie but a run of bogeys on the seventh, eighth and ninth left him struggling after his playing partner Mickelson had enjoyed a fast start.
Mickelson birdied the second and fourth holes to draw level with Woods. A further birdie on the fifth, followed by an eagle on the sixth, catapulted him to the top of the leaderboard as Wi, who four-putted the first to drop two shots, let further shots go on the fifth and sixth.
Woods rolled in a 13-foot putt for par on the 10th to stop his run of bogeys, then looked set to make a significant inroad into Mickelson's lead on the 12th.

The 14-time major winner holed a bunker shot for a birdie on the par-three but his hopes of a two-shot swing were abruptly ended when Mickelson drained a 30-foot par putt to stay four clear of his playing partner.
Mickelson then knocked in birdie putts from two and six feet on the next two holes to further extend his advantage, while Woods bogeyed the par-five 14th after a wayward approach.