Brendon de Jonge (69), Boo Weekley (67), Craig Bowden (68), Chris Anderson (70) and Glen Day (70) are knotted in second place at 4-under-par 136.
The wind is howling at Irondequoit Country Club on a track that has proven to be difficult this week. The pins are tight and the greens are quicker, so only 40 players are below par through 36 holes.
'This is how we should playing every week out here,' said Johnson. 'If you hit a good shot, the ball stays. If you don't, it doesn't. That's what we need to be playing. That's what we play on the PGA TOUR.'
Johnson began his second round on the back nine and started with seven consecutive pars. He first broke into red figures with a 12-foot birdie putt at the 17th, but lost that stroke thanks to a bogey at the par-4 closing hole.
Johnson parred No. 1, then hit a 6-iron to 12 feet to set up a birdie at the par-3 second. He parred the next two, then hit an 8-iron to 12 feet to register another birdie at the fifth.
Trouble loomed for Johnson at the 475-yard, par-4 seventh. He landed in a right-hand bunker and could not get up and down to save par. Johnson fell to 5 under par for the championship, but things picked up down the stretch.
He appeared headed for another bogey at the eighth, but drained a 20-foot par putt. At the par-5 ninth, Johnson got up and down for a final birdie to move his advantage to two shots.
'I didn't really hit it very well today,' admitted Johnson. 'But I putted well so I'm happy with that. You just grind it away, see what happens and see where the scores are at the end of the day.'
Along with praising the course, Johnson also acknowledged that the heavy wind has held back low scoring.
'It's so confusing out there,' acknowledged Johnson. 'We charted the golf course and you should know where everything is and you really don't. It's blowing from some direction. I'm just not sure.'
Kevin Stadler (68), Steve Collins (68), Jarrod Lyle (69), Chris Baryla (70), Jim McGovern (69), Gary Christian (71), Chez Reavie (69), David Hearn (68), Pat Bates (70) and Scott Gardiner (65) are knotted in seventh place at 3-under-par 137.
The 36-hole cut fell at 1-over-par 141 and defending champion Rick Price barely made it to the weekend. He posted a 3-over 73 on Friday to finish two rounds at even-par 140.