Lingmerth, who edged out Justin Rose at the third play-off hole two years ago, again displayed his liking for the Jack Nicklaus layout as he birdied the first and reeled off four in a row from the fifth, although further gains at 11 and 13 were offset by mistakes at the 10th and 12th.
Dufner recorded just one bogey on his seven under par round of 65 and sank an eagle on the par five seventh.
Former US PGA champion Dufner fired six birdies and an eagle to leave himself one shot clear of Sweden's Lingmerth heading to the 18th hole. Johnson's six-over par 78 didn't include a single birdie.
"I caught some breaks when I missed the fairway and still had some fairly good opportunities from the rough", Lingmerth said.
"It's a very humbling game", he said.
Spieth, who finished with a share of second at Colonial Country Club in Texas on Sunday, teed off on 10 and followed three birdies in his first six holes with back-to-back bogeys. "There's a lot of work ahead this week and weeks to come obviously so I'm just trying to take one shot at a time".
Jordan Spieth and Daniel Summerhays are a shot further back on six under but defending champion William McGirt is off the pace after carding a 71. The world's No. 1 player three-putted the par-3 16th after hitting into the water and made triple bogey.