Kevin Na, who shared the second-round lead with Mickelson, carded a 1-under 70. He stands at 10-under-par 203. K.J. Choi and Harrison Frazar each carded third-round 66s to move to 9-under-par 204. They were joined in a tie for third place by Steve Flesch (67) and Kenny Perry (67).
The third round at TPC of Scottsdale was played in front a tournemant-record crowd of 165,168 fans.
Mickelson, who played his college golf at nearby Arizona State, got off to a quick start with a birdie at the first. Lefty later rolled in 12-foot birdie putt at the fifth to move one stroke clear of Na.
The reigning Masters champion made it two straight as he drained a 14-foot birdie try at six to move two clear of Na. Mickelson three-putted for bogey at the par-4 10th to slip to minus-11 and into a share of the lead with Na.
Na chipped in for birdie at the 11th from just off the green to move one stroke ahead of Mickelson. However, Na missed the green at the 12th and that led to a bogey and dropped him into a tie with Mickelson atop the leaderboard.
Mickelson, whose last official win came at Augusta, moved to minus-12 when he two-putted for birdie at the 13th. Na, who also birdied the 13th, dropped out of a share of the lead when he bogeyed the par-5 15th. He lost his second shot left into water, then missed a 4-foot par putt.
Mickelson, a playoff winner here in 1996, put more room between himself and Na when he birdied the 17th from 3 feet out to move to 13 under. Lefty closed in style as he drained a 15-foot birdie putt at the last.
'The birdie on 17 for me was the biggest one because I can drive the green,' said Mickelson. 'You feel like you need to make birdie there, so I don't feel like I gave a shot back. If I don't birdie 18, you feel like you give one back. I made the putt. It doesn't change my mindset any, if I was three ahead or four ahead, but it's nice to have that extra shot in hand.'
This is the 15th time Mickelson has held at least a share of the lead after 54 holes. He has gone on to win 10 of the first 14 tournaments.
'Well, it was a fun round. There was a lot of people out there,' Mickelson said. 'It felt like I shot over par compared to yesterday, but it was good enough to get in the lead, and I'm looking forward to Sunday's round. It's so much fun to play in the last group in this event.'
Na played the opening 10 holes at 2 under thanks to three birdies and one bogey. After his bogey at 15, Na's struggles continued at the next. On the raucous par-3 16th, Na three-putted from 60 feet out for bogey.
The South Korea native missed a 7-foot birdie putt at the 17th. Na closed with an up-and-down par at the last to end four shots off the pace.
'It was a long day. It was tough,' Na said. 'I felt like I played really well. I think the only hole I'd want to start replaying is 15. I was playing solid until right up there. But I think from there things went a little wrong. From there, with the crowd pulling for Phil so much, it kind of shook me up a little bit and affected me on the last couple holes.'
Mark Calcavecchia, a three-time winner here, carded a 6-under 65 Saturday. He was joined in a tie for seventh place at 8-under-par 205 by 2001 PGA Championship winner David Toms.
Tim Herron and Charles Warren are one stroke further back at minus-7. Stewart Cink, Scott McCarron, Shaun Micheel and Scott Verplank share 11th place at 6-under-par 207.
World No. 1 Vijay Singh climbed the leaderboard with a third-round 66. He stands in a tie for 23rd at 4-under-par 209. Jonathan Kaye, the defending champion, is well off the pace at minus-1.