Joe Daley fired an 8-under 64 to move to 16-under-par 200. He shares third place with James Nitties, who carded a 5-under 67. Troy Matteson, Jerry Smith and Willie Wood are one stroke further back at minus-15.
Wagner, who is in search of his first tour win, got off to a rough start with a double bogey at the third and a bogey on No. 4 at the Black Creek Club. The 25-year-old quickly erased those mistakes though.
'I'm thinking, I'm 3 over on this course. I love this course and I've never been over-par out here,' said Wagner. 'It was frustrating. I was a little nervous and a little worried. I wanted to get back into contention.'
He drained a birdie try on the fifth and made it two straight as he birdied the par-5 sixth. Wagner, the runner-up here last year, birdied seven and eight as well. He closed out the front nine with another birdie to cap a run of five straight birdies to make the turn at 13 under.
Wagner rolled in a 30-foot birdie at the par-4 13th and came right back with a 2-foot eagle putt on the 14th to jump to 6 under and a share of the lead. The former Virginia Tech Hokie moved to the top of the leaderboard with a two-putt birdie on the par-5 closing hole.
'I wanted to be in one of the last groups,' said Wagner. 'I've never won out here before so honestly it might be more comfortable for me to come from behind. I know no matter what happens tomorrow at the start, I know I can still come back because I've done it before and I can do it again.'
Schultz, who is also gunning for his first Nationwide Tour win, opened with a birdie on the third. However, he stumbled to bogeys on the fourth and sixth to drop to minus-10.
'You've got to make birdies on this course and I knew it was going to be 20-something under to win,' said Schultz. 'I'm standing on the 10th tee at 10 under thinking it's now or never. I know I can play well on the back because I have all week.'
The 32-year-old ran off three straight birdies from the 10th to atone for those bogeys. Schultz dropped another stroke on the 13th, but then eagled the par-5 14th to move to 14 under.
Schultz ran home birdie putts on 15 and 16 to get within one stroke of the lead. Like Wagner, Schultz birdied the last to end at 17 under.
Nathan Green posted an 8-under 64 to move to 14-under-par 202. He was joined in a tie for eighth place by Scott Petersen, Grant Waite, Scott Weatherly and Ben Bates.
David McKenzie, Esteban Toledo, Bubba Watson and Robert Hamilton are one stroke further back at minus-13. Second-round leader Mathew Goggin struggled to a 2-over 74. He fell into a tie for 17th at minus-12.