After Johnson was assessed a drive-through penalty for jumping the final restart - a sanction Johnson protested vehmently - Stewart passed Juan Pablo Montoya on Lap 398 of 400 to win Sunday's FedEx 400 benefiting Autism Speaks at Dover International Speedway.
The victory was the first of the season and third at Dover for Stewart, who has notched 42 of his 48 career wins after May 31. Stewart finished .788 seconds ahead of Montoya, who matched his career-best NASCAR Sprint Cup Series finish on an oval track.
Jeff Gordon came home third, followed by Kyle Busch and reigning Cup champion Brad Keselowski. Johnson finished 17th, the first car one lap down, smarting from a penalty he felt was unjustified.
But Keselowski's Ford failed the height-stick test in postrace inspection (too low in the front), with penalties expected after NASCAR's completion meeting during the coming week.
Stewart, whose struggles this year have been well-documented, was happy to take the win, no matter how it came his way. Coming on the heels of a seventh-place run last week at Charlotte, a 1.5-mile downforce track, Stewart was happy to point out the progress his team is making.
"It's definitely momentum," Stewart said. "We got two weeks of momentum under our belt now at two totally different race tracks. That is big. Momentum is huge in this sport. We've still got a lot of work to do. We won't sit… I guarantee you none of these guys behind you (his crew) will tell you we are exactly where we want to be right now. It's a good reward for how hard they have been working to get that first win of the year.
"Now it's trying to be more consistent and stay in the top 10 more and make our program better. It's proof that no matter how bad it's been this year, none of these guys have quit and given up. Just really proud of the effort this weekend; I think we probably made more gains from Friday to right now than any team in the garage did. I'm really proud of that fact."
If Stewart was elated after the race, Johnson was still fuming.
"I totally disagree with the call, but it is what it is, and we'll just come back and try to win in the fall," he said.
Johnson knew he had beaten Montoya to the start/finish line, not knowing whether something was wrong with Montoya's car, and said he tried to give the position back to the Colombian driver.
"I ran half-throttle for the first half a lap, waiting for him, and then at some point you've got to go, and you've got to race, and that's when I got back in the gas and took off," he explained. "I was hoping they would see that I was trying to give him the spot back."
NASCAR vice president Robin Pemberton, however, described the penalty as cut-and-dry.
"That was an easy call - a very easy call," Pemberton said. "He beat the 42 even out of the (restart) box, from what we could see on the film, we give ‘em an opportunity to give it back."
Until the decisive penalty, it looked for all the world as if Johnson would claim a record eighth victory at the Monster Mile.
Johnson started 24th and, in the early stages of the race, had difficulty moving forward through traffic. In fact, the No. 48 Chevrolet SS went a lap down when Kyle Busch passed him on Lap 70.
But Johnson came to pit road early, on Lap 71, and used the extra time on new tires to regain the lost lap by the time NASCAR called an opportune caution for debris in Turn 2 on Lap 80. From that point on, it was a charge to the front by the five-time champion.
Johnson had worked his way up to sixth before a caution for debris on the backstretch slowed the field on Lap 160, moments after a blown engine eliminated what was arguably the strongest car in the race, Matt Kenseth's No. 20 Toyota.
After a restart on Lap 165, Johnson again moved forward, finally taking the lead for the first time on Lap 206, passing Kyle Busch to the inside through Turns 1 and 2.
Just as a Johnson victory was looking academic, however, Denny Hamlin's right front tire blew in Turn 1 and sent his No. 11 Toyota hard into the outside wall, bringing out the seventh caution of the race. Montoya took two tires when the lead-lap cars came to pit road and narrowly beat Johnson to the exit.
That turned the race inside-out, as NASCAR black-flagged Johnson for beating Montoya to the start/finish line on the restart on Lap 382. Montoya held off Stewart for 16 laps but wore out his tires in the process and had to surrender the top spot.
"In one of the runs under green, we decided to make a couple of big changes on the car, and the car just took off - came to life," Montoya said. "It came to life at the right time. It's a shame there at the end that it was way too loose. I just couldn't hold Tony off."
Notes: Despite running 17th, Johnson holds a 30-point lead over second-place Carl Edwards (14th Sunday) in the series standings… Kyle Busch, who has two victories this season, moved back into ninth place after falling out of the top 10 last week at Charlotte… Hamlin's crash put a serious crimp in his effort to qualify for the Chase for the NASCAR Sprint Cup despite missing four races with a back injury. Hamlin dropped two spots to 26th in the standings and is 74 points behind Ryan Newman in 20th, the position he needs to reach to be eligible for a Chase wild card.