MacIntyre, who is making his debut in the $10.5 million event, was two up on the reigning Masters champion with three holes to play following a brilliant burst around the turn at Austin Country Club.
But, showing the class that has earned him six WGC title triumphs, Johnson eagled the 16th then rolled in a 17-foot birdie putt as a terrific tussle ended up all square.
It leaves the duo locked together on one-and-a-half points heading into the final group-stage games on Friday.
“You know, he holed putts when he had to hole putts,” said MacIntyre, who was round in four-under and bogey-free, afterwards. “He does that to win majors. I'm young. I've got plenty of time ahead of me.
“Obviously I was dying to win that match. I was in such a great position to do it. But he threw everything at me, and I can be proud of finishing all square. But obviously inside I'm a little disappointed not to win.
“But, once we walk away from here and get in the car and drive back to the house, it's going to be, you know what, I can compete with these best guys on the planet.”
Offering his reaction, Johnson admitted: “It was a tough match. Ended up making a really good halve, and definitely pleased with it.”
As had been the case in his first-day win over Kevin Na, MacIntyre lost the opening hole as Johnson got off to a flying start by hitting his approach from 85 yards to around three feet and knocking in the birdie putt.
It was also a case of deja vu, though, as the young Scot hit back straight away, winning the second on this occasion with a par-4 after Johnson’s second shot ended up close to a boundary wall and had to take a penalty drop.
Johnson, who made heavy weather of beating Adam Long by two holes in his opening encounter, then rolled in a 30-foot birdie putt at the third to quickly regain the upper hand before MacIntyre twice dug deep to stop him increasing his advantage.
First, the left-hander showed nerves of steel to hole a seven-footer for a halve in birdie-4s at the sixth then, from more than 60 feet from the hole, he got up and down from a bunker to share the next in par-3s.
After Johnson had missed the green right with his second at the eighth, it was MacIntyre’s turn to be in a promising position but the American salvaged the situation by holing from close to 12 feet for a fifth halve on the trot after his opponent had been unable to convert from marginally further away for a birdie.
There was nothing Johnson could do, though, to stop the Cyprus Showdown champion getting back to all square by the turn as MacIntyre hit his second at the par-4 ninth from 119 yards to seven feet and confidently rolled in the birdie putt.
The Scot followed that by converting a 22-footer at the par-4 tenth as he made it back-to-back birdies and, with Johnson being unable to follow him in from around 14 feet, the Scot had his nose in front for the first time.
After a lengthy wait on the tee, MacIntyre safely found the green at the short 11th and won that as well as Johnson found water on the left and, despite a valiant effort as his third shot almost found the hole, was unable to salvage the situation.
After winning the long 12th with a two-putt birdie, Johnson was left off the hook following a duffed chip as MacIntyre’s seven-foot birdie attempt slipped past the edge at the 13th.However, the Scot’s cushion was soon restored as Johnson was long with his approach at the 14th, didn’t reach the green with a difficult pitch and eventually conceded the hole before then showing why he is world No 1.
“I thought I played a great round of golf,” added MacIntyre, who takes on Adam Long in his next match while Johnson faces Na. “He showed why he's world No 1, but he had to work his very best in the end to match me, and that's something I can be proud of.”
In both his matches so far, MacIntyre has played his best golf in a run of events in the US that is all but certain to include a Masters debut in a fortnight’s time.
“I haven't had my golf game for the last kind of three and a half weeks, but this week it showed up,” said the former Scottish Amateur champion.
“I've got my coach (David Burns} out. We worked hard at Sawgrass last week. We played a lot of holes in practice this week. It's really shown.
“I'm committing to every golf shot I've got in front of me. My tee-to-green game is finally back, and I'm putting it well. Just unfortunate the ball didn't go in the hole the last couple, but that's golf.”
The Scot was already on Padraig Harrington’s Ryder Cup radar before this week, but said of his hopes of making the European team at Whistling Straits in September: “I've got a long way to go.
“I've only just tied against Dustin there today, but, you know what, I'm going to play the same way I play with one of my friends if we're having a wee game back home. It's the same kind of fire. Nothing changes.
“If the Ryder Cup happens, the Ryder Cup happens. I can't control what the selectors do or if I'm going to get in that team. I think I have to get in it with no questions asked.
“I've just got to go out here, play my golf and just now I'm playing some of the best golf I've played in a long time, and that's how I want to play.”
World No 2 Justin Thomas and US PGA champion Collin Morikawa are already out of the reckoning for the knock-out stage but Rory McIlroy still has an outside chance of progressing.
The four-time major winner bounced back from his heavy first-day defeat against Ian Poulter by producing a confidence-boosting effort in beating Lanto Griffin 4&3.
But, after beating Australian Cameron Smith to make it two wins out of two, Ryder Cup talisman Poulter is the favourite to win that group heading into the final matches.
Other players with 100 per cent records include Spanish duo Sergio Garcia and Jon Rahm, defending champion Kevin Kisner and South African Dylan Frittelli.
Full second-day results
Dustin Johnson halved with Bob MacIntyre
Adam Long bt Kevin Na 2&1
Justin Thomas lost to Kevin Kisner 2&1
Matt Kuchar bt Louis Oosthuizen one hole
Jon Rahm bt Shane Lowry two holes
Sebastián Muñoz lost to Ryan Palmer 2&1
Collin Morikawa lost to Max Homa 2&1
J.T. Poston bt Billy Horschel 4&2
Bryson DeChambeau bt Si Woo Kim 2&1
Antoine Rozner lost to Tommy Fleetwood 4&3
Xander Schauffele bt Jason Day 2&1
Andy Sullivan halved with Scottie Scheffler
Patrick Reed bt Christiaan Bezuidenhout 2&1
Bubba Watson halved with Joaquin Niemann
Tyrrell Hatton lost to Sergio Garcia 3&2
Matt Wallace lost to Lee Westwood 5&3
Webb Simpson lost to Mackenzie Hughes 4&3
Talor Gooch lost to Paul Casey 3&2
Patrick Cantlay bt Carlos Ortizone hole
Brian Harman bt Hideki Matsuyama one hole
Rory McIlroy bt Lanto Griffin 4&3
Ian Poulter bt Cameron Smith one hole
Tony Finau halved with Will Zalatoris
Dylan Frittelli bt Jason Kokrak 3&2
Viktor Hovland lost to Bernd Wiesberger 4&2
Kevin Streelman lost to Abraham Ancer 2&1
Daniel Berger lost to Brendon Todd 2&1
Erik van Rooyen bt Harris English 2&1
Matt Fitzpatrick bt Corey Conners 5&4
Jordan Spieth halved with Matthew Wolff
Sungjae Im lost to Marc Leishman 2&1
Russell Henley bt Victor Perez 4&3
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