The outside lane was more organized as the final lap unfolded, and Jones got a strong run through Turns 1 and 2.
Kyle Larson, who won the Xfinity Series race Friday night, was out in a crash with Stenhouse.
Ricky Stenhouse Junior was involved in a number of the on-track incidents Saturday that led to ten yellow flags.
"How about that race boys and girls?" said Jones, who replaced 2004 series champion Matt Kenseth at Joe Gibbs Racing this year.
Jones was involved in one of the many wrecks, but his No. 20 Toyota was still in good enough shape to get by Truex late.More news: "Pay $200,000 For Overtime": Former Donald Trump Driver Sues His Company
Asked if Jones' victory was a momentum-builder for the next generation, third-place finisher AJ Allmendinger cracked, "One of those three are going to win next week, so I don't know".
"I think it's a little bit typical plate racing, " reigning Daytona 500 champion Austin Dillon told NBC Sports after Saturday's Cup race.
"I should have wrecked him and sent a message to the whole field". Stage One top 10 was as follows #17Ricky Stenhouse Jr, #18 Kyle Busch, #42 Kyle Larson, #24 William Byron, #9 Chase Elliott, #41 Kurt Busch, #31 Ryan Newman, #2 Brad Keselowski, #3 Austin Dillon, and #88 Alex Bowman rounded out the top 10.
Logano (one win) and Hamlin (winless) have come oh-so-close before to winning the title, and an Elliott championship would link today's fans with the old-school loyalists who loved rooting for his dad, "Awesome" Bill Elliott. "I think 13th will be an okay starting spot".
Truex called Jones "a good kid" but said he did not give him an inch. He's worked hard. I don't know the repercussions of him winning here, what they're going to be. So happy for him, happy for his family and his fans.More news: 'Miracle': Montana Authorities Find Abandoned Infant Alive Who Was Buried
"The 17 (Stenhouse Jr.) turned the 2 (Brad Keselowski) and then that was it", said Denny Hamlin of the first melee that involved almost half the field.
Chevrolet extended its winless streak to 17 races, its longest since a 31-race drought in 1981-82. It's been a tradition for each Daytona 500 champ since 1996.
In fact, he went as far as saying that he "should have wrecked" William Byron, who used risky blocking maneuvers that collected several cars in one of the crashes.
Daniels is believed to be the first female black crew member to compete in a NASCAR national series event.
Still, Stenhouse managed to lead 51 laps during the race - more than twice as many as any other driver.More news: We'll show Thierry Henry he picked the wrong side
"Everybody blocks as much as that, so I don't see any difference in it. 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".
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