Defending champion Ben Crane (69), Craig Bowden (71) and Tim Petrovic (70) share second place at 7-under-par 137. Scott Hend carded a 6-under 66 and is tied with Brian Gay, who shot a 2-under 70 on Friday. That duo is knotted at minus-six.
For the second consecutive day, heavy winds and cool temperatures greeted the players in the final tune-up for next week's first major of the season, The Masters.
Johnson, the Nationwide Tour Player of the Year in 2003, who had a late tee time on Friday, traded a birdie for a bogey on his first nine, the back side at Sugarloaf. He ran home a 25-foot eagle putt at the closing hole to reach 5 under par for the championship.
He parred his first three holes on his second nine, but leapt up the leaderboard with his play, starting at the fourth. Johnson had a severe sidehill lie at the par-5 hole but knocked his third to inches for the tap-in birdie.
Johnson collected another birdie at the fifth when he sank a 7-footer. He made it three in a row at No. 6 with a 10-footer and now the Nationwide Tour alumnus was alone in first at minus-8.
Johnson birdied the par-4 ninth to grab a two-shot lead heading into the weekend, his first on the PGA Tour.
'I'm just going to try to keep doing what I'm doing,' said Johnson. 'One of my goals this year on the tour was to get comfortable out here like I was last year. I feel like I am now.'
Bowden opened on the back nine Friday and immediately went into red figures. He hit a pitching-wedge 25 feet past the hole and sank the birdie putt, but trouble loomed four holes later. At the 14th, Bowden hit his approach to the short right portion of the green and three-putted for bogey.
Bowden, a 35-year-old from Indiana, nearly holed out his 5-iron from the fairway at the 17th. Instead he kicked in his short birdie putt to make the turn at 1-under 35.
At the fourth, Bowden knocked his birdie try three feet past the hole and missed the comeback putt for another bogey. He made up for it at the next hole when he roped a 4-iron 6 feet short of the hole and cashed in on the birdie try.
'It's been a tough two days so far,' said Bowden. 'I'm obviously very pleased with the way I'm sitting, but, you know, it's just it's a good golf course and it's a hard golf course.
'The wind is swirling big time. It's tough to pick a club and then commit to it because there's a few holes out here that you can have a train wreck on.'
Bowden, a winner on the Nationwide Tour last year, is one of those players who is not gearing up his game for Augusta next week. He is not in the field next week for The Masters, but wants win No. 1 at Sugarloaf.
'It's still a golf tournament to me,' said Bowden, whose best finish on tour this year was a tie for 13th at the Honda Classic. 'I don't care who is playing in the field. They are paying $800,000 this week. If I'm the only guy that shows up, that's my fortune.'
Petrovic was 3 under on his round when he made it to the 18th, his ninth of the round. At the par-5 hole, he horribly missed a par putt and instead of taking advantage of the par-5 he left with bogey to fall to minus-7.
Petrovic missed another par putt at the first, from about 2 feet and that left the Massachusetts native stunned.
'Now I'm thinking, what is going on here? It's like a conspiracy.'
Petrovic rallied with back-to-back birdies at 5 and 6, but the wheels came off again.
He bogeyed the seventh, then three-putted from 50-feet for his second consecutive bogey. Petrovic birdied the final hole to polish off his round of 70.
'I was grinding a little bit,' admitted Petrovic. 'I was kind of wearing myself, giving myself a tough time inside. I just have to go out and do my business and play my own game.'
Crane tallied two bogeys in his first three holes but collected five birdies the rest of the way for his share of second place.
Reigning PGA Champion Shaun Micheel (72) and Europe's top-ranked golfer Padraig Harrington (69) share seventh place at 5-under-par 139.
The two co-leaders after Thursday's opening round did not fare well on Friday. Jose Maria Olazabal posted a 5-over 77 and is part of a group in 17th at 2-under-par 142, while Roger Tambellini carded a 78 and is tied for 25th at minus-1.
Phil Mickelson shot an even-par 72 and shares 13th at 3-under-par 141.
The 36-hole cut fell at 1-over-par 145 and among the notable players who will miss the weekend are Matt Kuchar (147), U.S. Ryder Cup captain Hal Sutton (148) and David Toms (155).