A race that was Johnson's to lose ultimately became Kenseth's series-high fourth victory of the season after crew chief Jason Ratcliff passed on putting new tires on the No. 20 Toyota following the race's ninth caution.
"I thought he was slightly crazy when that happened," said Kenseth, who widened his lead when the field went four-wide after the restart on lap 246 and saw Johnson's No. 48 Chevy spin from second place on a dominant day he led three times for 182 of 267 laps.
"I didn't think there was any way that we were going to hold on for that win. He made the right call at the right time and those guys got it done."
Kenseth led twice for 38 laps, including the final 23. Johnson, the five-time champion and current series points leader, finished ninth and leads Carl Edwards by 38.
The restart bothered Johnson, who accused Kenseth of breaking the pace car speed. But he took solace in salvaging his 11th top-10 despite between sandwiched in the logjam that could have been worse.
"We were kind of in an awkward situation in that restart there," he said. "We were like three- and four-wide going in the corner, then something happened with the air and just kind of turned me around. Unfortunate, but at least we rallied back for a good finish."
Rain on Saturday forced NASCAR officials to postpone the race to a daytime start.
The event was red-flagged for 18 minutes following a seven-car wreck involving defending race and Sprint Cup winner Brad Keselowski, who returned to finish 33rd. It was the biggest incident of 10 cautions for 42 laps, but things were clean after Johnson brought out the final yellow flag.
The checkered flag crowned Kentucky's third different champion in as many events though Kenseth, like Johnson, was due for a breakthrough on the 1.5-mile oval.
He finished seventh here last year and sixth in the 2011 inaugural race. However, victory didn't seem likely for the 2003 Cup champion after qualifying 16th and running outside the top 20 during the first quarter of the event.
"I thought our first run, we were all right and I guess probably after the second run, we were able to move forward pretty good," Kenseth said. "I felt pretty good about what we had. I thought we need to get it better."
From then on, the first-year Joe Gibbs Racing driver was a perennial top-five contender. Trouble was, he and other hopefuls seemed to need Johnson to suffer misfortune to have any shot of catching him. The way he was running, that appeared unlikely.
Turns out, Kenseth needed to rely on the left-side tires Ratcliff ordered the previous stop. Taking fuel only the final time allowed him to gain the lead coming off pit road, and the rubber held up on the rough, bumpy track, both on the restart and through the final laps.
Ratcliff was shocked that more teams didn't follow suit with that strategy.
"I felt like more guys would make that call, and so I thought it was worth a shot to get out there," the crew chief said. "When we rolled off pit road and saw what everybody did, I looked to the guy beside me and I'm like, 'I can't believe we are the only ones that did that.' "
The decision led to a surprising late turn of events, and the tense finish in which McMurray and Bowyer took turns trying to chase down Kenseth provided a nice makeup after Saturday night's washout.
In a season of struggles, McMurray was just happy with his first top-five.
"Every week it's been something," he said, "so it's nice to have some good luck."
Bowyer remained third in points and gave Michael Waltrip Racing its second straight top-two run following teammate Martin Truex's road win last week in Sonoma, Calif.
Kenseth's victory meanwhile typified a weekend where a number of drivers were projected to win at Kentucky.
Friday's pole qualifying generated enough excitement for the series' third visit, with eight drivers breaking Johnson's year-old track record of 181.818 mph. The group included the five-time champion, who shattered his own mark at 183.144 mph before Hendrick Motorsports teammate Dale Earnhardt Jr.'s 183.636 mph speed in the No. 88 Chevy snatched the record and the pole, leaving Johnson to settle for the third spot.
Earnhardt's objective was ending a 37-race drought and improving his seventh-place points standing coming in. Earnhardt succeeded with the latter, finishing 12th to gain a spot with nine races remaining in NASCAR's regular season.
Johnson eventually picked up where he left off in practice and qualifying, becoming the story on Sunday with the best car after several early lead changes.
Edwards quickly got past Earnhardt after the green flag and led the first 32 laps, although a competition caution allowed Earnhardt to reclaim the lead with a two-tire stop, a strategy followed by the top 10. Denny Hamlin was one of those and restarted sixth on lap 36, but he quickly had to return to the pits when his right front tire went down.
Hamlin's misfortune quickly created concern for Earnhardt and Johnson when the rubber slid off the tire rim during his exit and flew back on to the track. Earnhardt ran over it, bending his splitter's right side, before the tire flew off and bounced off Johnson's hood to bring out the race's second caution on lap 39.
A hard wreck later sent Hamlin to the infield care center and left him 35th.
"I had to take a moment when I got out of the car to kind of gather my thoughts because obviously I didn't feel that great," Hamlin said.
The biggest incident came on lap 49 when Kurt Busch spun out Keselowski near turn 1, triggering an accident that red-flagged the race. Greg Biffle slammed into Keselowski, lifting his car off the asphalt and leaving both Fords mangled.
Somehow, both returned to finish 33rd and 34th respectively.
But at the time of the wreck Johnson had already taken his first lead of the race and appeared headed to a walkover victory before Ratcliff's risk resulted in Kenseth's reward.