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Six strokes behind South Korean Wi going into the final round at Pebble Beach Golf Links, Mickelson fired a flawless eight-under-par 64 to clinch his 40th victory on the PGA Tour.
The American left-hander took control of the tournament with a stunning outward nine of five-under 31 and holed two monster par putts after the turn on the way to a 17-under total of 269.
"It feels awesome," a beaming Mickelson told the Golf Channel. "Hopefully it's just one of a few this year because I am starting to feel pretty good."
While Mickelson won the pro-am celebrity event for a fourth time, Woods had to settle for joint 15th place after closing with a five-bogey 75 in his bid for a first PGA Tour win in more than two years.
Wi, hunting a maiden title on the US circuit, dropped four shots in the first six holes but recovered well, a birdie-birdie-birdie finish giving him a 72 and outright second place at 15 under.
Woods had been poised for a last-day charge after shooting a 67 on Saturday but missed several putts from inside six feet to tumble out of contention at the same venue where he won the 2000 US Open by a record 15 shots.
"I didn't hit it as bad as the score indicated but I putted awful," the former world No 1 said. "As good as I felt on the greens yesterday was as bad as I felt bad today.
"I just could not see my lines, I couldn't get comfortable, I couldn't get the blade to swing. Anything that I tried to do wasn't working and consequently I made a ton of mistakes on the greens."
Mickelson, who had previously won the Pebble Beach National Pro-Am in 1998, 2005 and 2007, took full advantage of a poor front nine by the pacesetting Wi.
Three strokes ahead of the chasing pack overnight, the Korean made the worst possible start with a four-putt double-bogey on the opening hole.
He also stumbled with a bogey at the tricky par-three fifth after missing the green to the left off the tee, to drop back into a tie for the lead at 12 under.
Mickelson had charged to the top with birdies at the second, fourth and fifth, where he struck a superb mid-iron to just one foot.
He then rammed in a 21-footer to eagle the par-five sixth and vault two strokes clear with Woods, Kevin Streelmanand Kevin Na tied for second place.
Out in 31, Mickelson did well to save par at the short 12th, where he rolled in a 30-footer and Woods holed out from a greenside bunker for birdie.
With huge galleries following the two biggest names in US golf, Mickelson conjured an exquisite bouncing approach to just two feet at the par-four 13th, knocking in the birdie putt to regain a two-shot cushion.
Another birdie followed at the par-five 14th and he finished with yet another at the final hole to seal the win.
As he made his way to the scorer's tent, his wife Amy hugged him and said: "I am so happy for you. Oh my gosh! What a round. Are you kidding me?"
LEADING FINAL-ROUND SCORES (US unless stated)
269 - Phil Mickelson 70 65 70 64
271 - Charlie Wi (South Korea) 61 69 69 72
273 - Ricky Barnes 70 66 70 67
274 - Aaron Baddeley (Australia) 66 72 69 67
275 - Kevin Na 66 69 70 70, Dustin Johnson 63 72 70 70
276 - Padraig Harrington (Ireland) 68 66 72 70, Ken Duke 64 73 65 74
277 - Spencer Levin 69 69 71 68, Jimmy Walker 69 68 71 69, Jason Kokrak 68 67 72 70, Greg Owen (Britain) 68 67 72 70, Kevin Streelman 70 69 68 70, Brendon Todd 67 69 69 72
278 - Richard Lee 65 71 73 69, Steven Bowditch (Australia) 71 67 72 68, Hunter Mahan 65 70 70 73, Bob Estes 67 70 69 72, Tiger Woods 68 68 67 75
279 - Davis Love III 70 70 70 69, Robert Garrigus 68 69 71 71, Brian Gay 69 65 74 71, Brian Harman 64 73 71 71, Ryan Moore 72 64 71 72
280 - Danny Lee (New Zealand) 63 73 74 70, Vijay Singh (Fiji) 68 68 71 73, Geoff Ogilvy (Australia) 70 69 68 73, Kevin Stadler 69 70 73 68
281 - Miguel Carballo (Argentina) 69 71 69 72, Sean O'Hair 68 74 69 70, Zach Johnson 67 72 72 70, Brian Davis (Britain) 70 74 68 69, Ryan Palmer 72 71 64 74, Rocco Mediate 71 66 76 68
