It will be Dufner, whose only two PGA Tour victories came in the last four weeks, against the 2007 Masters champion who got the last of his seven wins two years ago at Hogan's Alley.
"It seems like one of us is either going to win or finish second," Dufner said after his 4-under 66 in the third round Saturday.
After two bogeys the previous three holes, Dufner matched playing partner Johnson's birdie putt on the 17th hole and overcame a wayward final tee shot to save par and keep the lead.
Dufner's 15-under 195 total put him a stroke ahead of Johnson, who shot 65. Tom Gillis was a distant third at 7 under after a 69.
"I really wasn't aware of (the separation) until I looked at the board on 13. It was more than I anticipated," Johnson said. "It seemed like I didn't hear too many roars in front of us, so that's a telling sign. ... I still have 18 holes and that's my focus. I totally anticipate Dufner to keep doing what he's doing. There's not a whole lot going on that's wrong."
Dufner, the winner last week in the Byron Nelson Championship about 30 miles away, is trying to win for the third time in his last four starts. He also is trying to do something only Ben Hogan has done.
Hogan, Dufner's hero, is the only player to win both PGA Tour events in the Dallas-Fort Worth area in the same year. When he did it in 1946, they weren't played in consecutive weeks.
The last player to win in consecutive weeks on the PGA Tour was Tiger Woods in 2009. Nobody won more than two tournaments last season.
Like Johnson, who wore a plaid-collared shirt Saturday, the first time Dufner realized the gap from everyone else had widened was when he saw that scoreboard at 156-yard 13th hole. And he had a three-stroke lead then.
"From that point on I kind of knew that ... we are going to be battling it out in kind of a unique situation," Dufner said. "The leaderboards here most of the year have been pretty packed and you got a lot of guys having a chance to win the title the last nine holes."
Dufner avoided a playoff at the Nelson with a 25-foot birdie on the 72nd hole. He has led or shared the lead after 12 of his last 35 rounds, including five of the last seven.
After bogeys at Nos. 14 and 16, Dufner's approach at the 379-yard 17th rolled about 8 feet from the flag.
Johnson, within a stroke of the lead after a 17-foot birdie at the par-3 16th, followed Dufner at No. 17 with a shot to the same spot - his ball up and stopped against the one already on the green. After a rules official sorted out the marks, Johnson curled in a birdie putt. Dufner then did the same to keep his lead.
When his final tee shot of the day went way left, closer to the 10th fairway than the 18th, Dufner got his next shot on the green and two-putted from 68 feet to save par.
Before winning at New Orleans on April 29, the 35-year-old Dufner was winless in his previous 163 PGA Tour starts. He then took a week off to get married, returned to play at The Players Championship before winning the Nelson.
Bo Van Pelt had his streak of 13 consecutive sub-par rounds at Hogan's Alley end with a 71. But he was fourth at 204, one ahead of John Huh and Ryan Palmer.
When Dufner and Johnson completed their first nine holes, they were tied at 13 under and had a five-stroke lead on the rest of the field. Dufner then had three straight birdies.
Dufner made a 20-foot birdie putt at the 386-yard 10th hole, where Johnson had his first two-putt of the round - from nearly 51 feet - to save par.
Dufner had a streak of 38 consecutive bogey-free holes snapped at the 449-yard 14th when he drove into the rough then missed the green with the second shot. But Johnson had his first three-putt of the tournament at the same hole, from 60 feet after his approach from a fairway bunker.
At No. 15, Johnson's second shot settled into a grassy clump only inches from rolling over a ledge into a ditch. With his feet together to keep from falling over himself, Johnson's pitch from about 81 feet rolled only inches from the cup to set up a tap-in par-saver.
Johnson needed only eight putts for a 31 on the front nine, though some of those putts were just to save par since he hit just three of those greens in regulation.
"Today was a battle as far as my ball-striking. With the exception one lucky shot on 15, I didn't put myself in terrible position," Johnson said. "I just scored. I think Dufner played better than I did, but I scored."
Divots: Masters runner-up Louis Oosthuizen opened his third round with four consecutive birdies. He was in a group of seven players tied for seventh, but 11 strokes behind Dufner. .. That group at 206 includes Kelly Kraft, the 2011 U.S. Amateur who turned pro after the Masters. The former SMU player was 6 under through his first eight holes and played even the rest of the round. ... Vijay Singh, who got the last of his 34 PGA Tour wins four years ago, was 4 under through six holes Saturday. He had four consecutive bogeys on the back nine.