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Stenhouse, 35, grabbed the lead for the first time in the race with a shove from Kyle Larson in the first overtime but a wreck involving Austin Dillon and William Byron sent the race into a second two-lap overtime.
As second overtime began, Logano edged ahead of Stenhouse but a big push from Christopher Bell sent Stenhouse ahead of Logano as Travis Pastrana and Aric Almirola wrecked, which brought the caution back out.
Since Stenhouse had already taken the white flag, the race was over and he was declared the winner.
“When (Kyle Busch) went to the bottom there I was able to push (Logano) and (Larson),” Stenhouse said of the first overtime. “We had a huge run. I was hoping we were going to get to the white (flag) there, and we didn’t, so I knew I was going to take the top.
“I was hoping (Logano) was going to follow, and he did. He was able to push us out. I went to the bottom, (Busch) and (Logano) got a huge run. Larson split me in the middle, but another fellow dirt racer with Bell gave me a good shot down the little short chute into (Turn) 1, and we were out front when the caution came out.
“We were out of fuel so the fuel light was going crazy. I hope y’all had fun. That was a heck of a race.”
It’s the first NASCAR Cup win for Stenhouse since 2017 and the third of his career. All three of his wins have some on superspeedways.
“Man, this is unbelievable,” Stenhouse said. “This was the site of my last win back in 2017. We’ve worked really hard. We had a couple shots last year to get a win and fell short.
“It was a tough season, but man, we got it done, Daytona 500.”
The race also set a record for length, going 212 laps or 530 miles.
Following the caution between Stages 2 and 3, most of the lead-lap cars all pit with Almirola first off pit road. Ross Chastain was penalized for speeding and had to restart from the rear of the field. Bell had to go to the back as well for running over equipment as did Noah Gragson for an uncontrolled tire.
On the restart on Lap 138, Bubba Wallace – who did not pit – led the way followed by Almirola, Buescher and Byron.
NASCAR was forced to display a caution on Lap 140 for debris in Turn 2, which was a blown tire from Ryan Blaney’s No. 12 Ford. Bowman also went for a half-spin when the caution came out.
The race resumed on Lap 144 with Almirola out front followed by Buescher, Kevin Harvick and Wallace. Buescher powered ahead to the lead on Lap 149.
Wallace, who had stayed out at the stage break, made his green-flag stop on Lap 172, pitting by himself.
A group of Fords pit on Lap 177 with Keselowski first off pit road. Toyotas pit on Lap 178 with Martin Truex Jr. first off pit road of that group.
The remainder of the field hit pit road on Lap 179 with Larson first off pit road. Stenhouse was caught speeding and had to serve a pass-through penalty.
Just as the cycle of green-flag stops was completed, Ryan Preece slowed down and got loose in the middle of the field, which triggered a multi-car wreck on Lap 182 that brought out the fifth caution of the race.
Harrison Burton, among the last group of cars to make their final green-flag stop, emerged as the leader. The race resumed on Lap 188 with Burton followed by Logano, Byron, Busch and Larson.
Allmendinger got a shove into the lead on Lap 189 for the first time in the race.
With help from his teammate, Buescher, Keselowski powered back to the lead with 10 laps to go.
With five laps remaining, a nine-car pack led the way out front with Keselowski still leading the way.
Busch, with help from some fellow Chevrolets, powered to the lead on the outside.
On Lap 198, Daniel Suarez off Turn 4 and ended up in the infield grass to bring out a caution and send the race into a two-lap overtime.
To start overtime, Busch led the way followed by Austin Dillon, Byron, Logano, Larson, Keselowski, Stenhouse and Buescher.
Entering Turn 3 after the restart, Byron got into Austin Dillon and spun him which triggered another multi-car wreck and sent the race into a second overtime. Stenhouse, who was getting pushed by Larson emerged as the leader.
To start the second overtime, Stenhouse was followed by Larson, Bell, Logano, Busch, Allmendinger, Denny Hamlin and Bowman.
Chastain just nipped Bowman racing side-by-side twelve-hundredths-of-a-second to take the Stage 2 win.
Logano was third, Stenhouse fourth and Cindric rounded out the top-five.
Following the caution between Stages 1 and 2, all the lead-lap cars elected to pit with Preece first off pit road.
The race returned to green on Lap 72 with Preece out front followed by Keselowski, Harvick, Almirola and Michael McDowell. Keselowski edged ahead on the restart.
With help from Cindric, Almirola took over the lead on Lap 77. A shove from Preece sent Keselowski back into the lead on Lap 82.
With 35 laps remaining in the stage, Keselowski remained out front followed by Preece and Harvick.
A contingent of Chevrolets hit pit road on Lap 107. Kyle Busch was penalized for speeding and had to serve a pass-through penalty.
Fords hit pit road on Lap 109. The remainder of the field pit on Laps 110 and 111.
Once the cycle of stops was completed on Lap 112, Logano emerged as the leader.
Buescher, riding the top lane with Gibbs behind him, edged out front on Lap 116. Logano, on the inside, got back out front on Lap 117.
Much of the field elected to pit under the caution but Logano remained on the track and inherited the lead. Both Jimmie Johnson and B.J. McLeod were penalized for speeding and had to restart from the rear of the field.
When the race resumed on Lap 125, Logano led the way followed by Truex, Chastain and Bowman.
With help from Bowman, Chastain moved into the lead on Lap 128.
With the help of his Ford teammates, Keselowski powered into the lead on the final lap and held off Preece to claim the Stage 1 win.
Buescher ended up third, Harvick fourth and McDowell rounded out the top-five.
Bowman started on the pole but Larson edged him at the line to lead Lap 1.
With a shove from Almirola, Bowman nosed back out front on Lap 2.
On Lap 11, Logano gave Larson a big push out to the lead as Bell moved into third. Bell went to the top lane and got around Larson for the lead on Lap 13.
Another shove from Logano allowed Larson to power back into the lead on Lap 21. Bowman answered with a shove of his own which sent Bell back to the lead on Lap 24.
Ty Dillon was forced to pit under green on Lap 27 with what appeared to be an engine issue.
Cindric shoved Almirola to the lead on the inside lane on Lap 35. Bowman edged ahead on Lap 36.
A group of Fords hit pit road on Lap 36 to make a green-flag pit stop for fuel-only. A group of Chevrolets followed on Lap 37.
The remainder of the field pit on Lap 38 with Herbst spinning out as he entered pit road. Herbst had to serve a pass-through penalty for a commitment line violation.
Once the cycle of stops was completed on Lap 41, Hamlin emerged as the leader followed by Bell and Reddick.
Chase Briscoe got around Hamlin on Lap 48 to take the lead as Hamlin remained close in the outside lane.
On Lap 52, just after Wallace drove to the lead, he received a hit from Truex on the backstretch and pounded the outside wall. Wallace was forced to pit under green with a flat tire as Truex inherited the lead.
With five laps to go in the stage, Truex remained out front leading a single-file line and was followed by Hamlin and Ty Gibbs.
Busch had to start the race from the rear of the field as he moved to a backup car following an accident in his Thursday night qualifying race.