A stroke in front of the chasing pack when the delayed first round was completed earlier in the day, the American left-hander carded a one-under-par 70 in breezy sunshine at Riviera Country Club.
Mickelson, who won his 40th PGA Tour title at the Pebble Beach National Pro-Am on Sunday, holed out with a lob wedge from the fairway to eagle the par-four eighth on the way to a six-under total of 136.
Pat Perez fired a six-birdie 65 to lie second, a stroke in front of fellow Americans Jimmy Walker (66), Jonathan Byrd (70) and Matt Kuchar (69), Swede Carl Pettersson (70) and Australian Jarrod Lyle (65).
Eight players were still out on the course when play was suspended in fading light, though all were well off the lead, and they will complete the second round early on Saturday.
"I probably didn't play the greatest today, but I was able to kind of salvage a good round and had a good break on eight," said Mickelson, who also recorded two birdies and three bogeys. "That was kind of a nice little bonus.
"I left myself uphill par putts on seven and nine, and that's really not a good thing to do here. If you're going to make five or six-footers, you really have to have them uphill where you can hit them aggressive enough to hold the line.
"They just kind of wobbled off, so I ended up missing those," added the four-times Major champion, who totalled 25 putts while hitting only eight of 18 greens in regulation.
Asked if he was disappointed he had not taken greater advantage of calmer conditions on Friday morning, Mickelson replied: "Maybe, but I also put myself in contention heading into the weekend, which is what my initial goal was.
"So with 36 holes to go I'm right in the thick of it," added the American, champion the tournament in 2008 and 2009. "I've got to go out and shoot some low scores because they're out there, but I gave myself a good opportunity."
Perez made the most of even more benign conditions on Friday afternoon, surging up the leaderboard with a flawless 66 that owed much to superb putting.
"I didn't drive it all that great, the 35-year-old American said after totalling only 25 putts but hitting just five of 14 fairways off the tee.
"I just scrambled well and I put myself in the right places to make par or birdie. Overall I just putted pretty well. I made the putts I had to."
Perez, who had to cope with strong gusting winds on Thursday morning in the opening round, was delighted to play in gorgeous afternoon sunshine on Friday with barely a breeze.
"It wasn't even comparable," he said. "Yesterday was 40 (degrees) and blowing 50 miles an hour at 6:00 in the morning. Today was warm and not much wind at all.
"When you're not freezing to death and it's not blowing 40, you think you can score pretty well."
British world number one Luke Donald carded a 72 to end the day six strokes off the pace, level with champion Aaron Baddeley of Australia (69) and American Joe Ogilvie, who aced the par-three 16th en route to a 71.
The cut was projected to fall at three-over 145 with Riviera fan favourite and twice winner Fred Couples, Australian Geoff Ogilvy and 2006 champion Rory Sabbatini of South Africa all likely to miss out.