Thanks to a push from Chris Buescher, Jones was able to get ahead of Truex Jr. and stretched the advantage to a couple of auto lengths as the field raced through Turns 3 and 4. Jones was one of the lucky ones who avoided major damage.
"It was a lot of hard work to be here", he said of Victory Lane.
Truex lapped the 2.5-mile tri-oval in 47.069 seconds at 191.209 miles per hour.
Jones, 22, beat Martin Truex Jr, AJ Allmendinger, Kasey Kahne and Chris Buescher in a two-lap shootout.
Shortly before that wreck on the initial would-be final lap, Kahne and Kevin Harvick were side-by-side with six laps to go when another wreck caused a significant delay with cars spread around the infield. "It's been so rewarding to be part of history while at the same time inspiring others to take on challenges they thought might not be possible".
How Jones Won: He was in position on the second overtime restart to get to the front and took advantage of the opportunity. "I didn't think we were going to have a shot to win this one about halfway".
Only nine races remain in the regular season.
Stenhouse finished 17th in the race and is 19 points out of the final playoff spot.
On Lap 54, Brad Keselowski was running behind leader William Byron when his No. 2 Ford turned off the front bumper of Ricky Stenhouse Jr.'s Fusion, slammed into the No. 41 of Kurt Busch and ignited a Turn 3 wreck that involved 24 cars and wiped out all three Team Penske entries, along with Kurt Busch, Denny Hamlin, Daniel Suarez and pole victor Chase Elliott.
Japan struggles in the wake of worst flooding in decades
Heavy rain was forecast to continue through Sunday in the west and the east, agency official Minako Sakurai told reporters. In the town of Uwajima in Ehime Prefecture, a 63-year-old man was buried alive in his house due to landslides.
Last year's race victor, Ricky Stenhouse Jr., had the most memorable run.
Added Logano: "When one vehicle sits sideways in front of the field at 200 miles per hour, you can't get through it".
JOHNSON PENALIZED: Jimmie Johnson, seeking to end a 40-race winless streak, was running up front with 40 laps to go when his crew serviced the vehicle outside its pit box.
"There was a ton of torn-up cars so I figured we'd be able to salvage something", Larson said, not knowing there would be a few more added to the wreckage by night's end.
Chase Elliott won the pole.
Hendrick teammate Alex Bowman joins Elliott on the front row.
After rookie William Byron took the lead, a wreck on the 57th didn't impact the front group. He pointed the finger at Byron, who moved down the track to put a late block on the No. 2 and forced Keselowski to check up.
Daytona 500 victor Austin Dillon didn't seem to be much of a factor, but he made it to the end of the night and finished ninth.
Chevrolet has been mostly noncompetitive since Austin Dillon won the season-opening Daytona 500 in February.