Mickelson left a birdie putt at the par-4 17th just short before sinking a birdie at No. 18 for the 60.
Mickelson's round of 12-under at the La Quinta Country Club still represents the 48-year-old American's lowest score in relation to par.
Australia's Curtis Luck was alone in third after firing a bogey-free round of eight-under 64.
Adam Hadwin and Steve Marino are another shot back in a share of 3rd while defending champion Jon Rahm is tied for 5th at 12 under and four from Mickelson's lead.
"I really didn't think that this was going to be a day that I was going to go low", said Mickelson, who tweeted prior to his round that he was "a bit rusty, but also fresh and ready to get started". Some days you have those days where it just clicked. This golf course, there's out of bounds close by, it's easy to make big mistakes and I was able to get away with the one or two poor swings.
"I'm starting to drive the ball a lot longer and straighter than I have in a while and so that sets up nicely for that course", Mickelson said.
"It was kind of a lucky day for me in the sense that I did not feel sharp heading in", said Mickelson, who is in his 28th year on the PGA Tour.
It was one of just 37 rounds of 60 in PGA Tour history, and Mickelson owns three of them.
The tournament victor in 2002 and 2004, Mickelson will play the Nicklaus Course on Friday and PGA West's adjacent Stadium Course - also the site of the final round - on Saturday.
"I feel like I can play it aggressively with the way I'm hitting it off the tee".
'And I hit a shot here or there and ended up making a putt and all of a sudden I was quite a few under par.
Marino had a hole-in-one on the seventh hole at La Quinta in a 65. Hadwin had a 66 at La Quinta, the course where he shot 59 two years ago.
European - Shane Lowry kept up his brilliant scoring on the par-3 holes at the Abu Dhabi Championship in shooting a 5-under 67 in the third round to extend his lead to three strokes.
One of my predictions for 2019 is that Phil Mickelson would fall out of the top 50 in the Official World Golf Rankings for the first time in 25 years.
Rose can expect stiff competition from Spain's defending champion Jon Rahm while two-time former victor Phil Mickelson is also in the field.