Kevin Chappell became the 11th player in PGA Tour history to shoot a sub-60 round with an 11-under-par 59 in the A Military Tribute at the Greenbrier in West Virginia.
Chappell, playing his first PGA Tour event for 10 months after having back surgery last November, missed an 11-foot putt on the 18th.
Had the putt gone in he would have equalled the lowest round of 58 on the PGA Tour – shot by Jim Furyk at the Travelers Championship in 2016.
"I couldn't be happier where I'm at or more proud of myself in what I did," Chappell said on Sky Sports.
— PGA TOUR (@PGATOUR) September 13, 2019
"Ten months ago I was on the couch and couldn't walk. So many people had a lot to do with getting me out here and getting me competitive.
"I haven't accomplished anything yet, there's a long weekend ahead, but this is a step in the right direction.
"I never stopped believing but it's nice to have the evidence and move forward."
Scheffler, in just his second round as a PGA Tour member, and Niemann had shot 62s with first-round leader Shelton firing a 65.
Adam Long is one further back on 12-under at the halfway stage.
Scotland's Martin Laird had a 68 to for a six-under total of 134, two shots inside the cut.
But Ireland's Seamus Power missed the cut by one stroke after a second-round 69.