SILVIS, July 12, 2014 (AFP) - Former Masters champion Johnson shot a four-under 67 while McGirt, who started his round on the 10th hole, fired a 66 at the Deere Run course to reach 12-under-par 130.
Johnson has 11 US PGA Tour wins, while McGirt is looking for his first tour victory.
"Once again, a pretty solid day. Aside from maybe one poor miss, pretty solid," Johnson said. "I didn't do anything too flashy. My short game was decent. My putting was great. Even the ones I missed were great."
Johnson Wagner bogeyed his final hole to fall out of a share of the lead. Wagner carded a 65 and he shares third place at 11-under with Australia's Steven Bowditch (67) and Brian Harman (68).
Three-time champion Steve Stricker (65), Rory Sabbatini (70), Ryan Moore (67) and former British Open winner Todd Hamilton (69) are tied for sixth at nine-under-par 133.
At the par-five 17th, Johnson reached the green in two and two-putted for birdie to take a one-shot lead. But he missed the 18th green with his approach and walked off with a closing bogey that dropped him into a tie for the lead.
He was pleased with his round overall.
"A lot of positives all around," he said. "I'm just really comfortable here. Any wind, for the most part, I'm comfortable and any conditions.
"The greens were receptive, so if you had the right yardage with the right club, there's some aggressive shots you can have out there. A day that I felt like I left some out there, but I felt like I stole a couple, too."
McGirt has missed the cut in five of his last eight tournaments but he looked sound on Friday. Even an equipment malfunction couldn't slow him down.
"I was very pleased with it," McGirt said. "I struggled early. I'm pretty sure I cracked my driver, but couldn't get a replacement.
"All in all, it was a solid day. Nothing really happened on the back side starting out, then I made the turn and (caught fire). I'll take two more just like."
McGirt made it two birdies in a row with a 13-foot putt on the 13th. That moved him to 13-under. He made bogey at the ninth, his last, to drop to 12-under.
Scores on Friday after the second round of the $4.7 million John Deere Classic (par 71, USA unless noted):
130 - Zach Johnson 63-67, William McGirt 64-66
131 - Steven Bowditch (AUS) 64-67, Johnson Wagner 66-65, Brian Harman 63-68
133 - Rory Sabbatini (RSA) 63-70, Steve Stricker 68-65, Ryan Moore 66-67, Todd Hamilton 64-69
134 - Charles Howell 66-68, Jerry Kelly 66-68, Kevin Na 68-66, Kevin Tway 65-69, Bud Cauley 67-67, Robert Streb 65-69
135 - Stewart Cink 69-66, J.J. Henry 68-67, David Toms 65-70, Tim Clark (RSA) 72-63, Jordan Spieth 71-64
136 - Bo Van Pelt 67-69, Justin Hicks 66-70, Alex Prugh 68-68, Wes Roach 67-69