Elliott led the final 32 laps of the race, holding off a hard-charging Martin Truex Jr, who ultimately ran out of gas.
Truex closed to the back bumper of Elliott's No. 9 Chevy as his vehicle moved wide heading out of the first turn of the final lap, but Elliott regrouped and pulled away as Truex sputtered home second, out of fuel. Stewart, with eight career road course wins, won three straight from 2004-05.
Elliott made the pass on lap 27, bringing the sellout crowd to its feet.
Midway through the segment, the Big 3 were running in the top 10, but Elliott dominated and beat Busch by 1.3 seconds.
Suarez and Jones finished fourth and fifth, respectively, on Sunday. "Jimmie (Johnson) has been one of my heroes for a long, long time".More news: Hall wins Women's British Open for 1st major title
Moments later, Joey Logano slid off course on lap two and dropped to the rear of the field, then headed to the garage with a broken radiator, his day done. On Sunday, The Glen figures to be a prime spot for the likes of Daniel Suarez and AJ Allmendinger to try and win their way into the postseason.
Elliott led Truex by 1.1 seconds with 19 laps left, Jones was third over 10 seconds behind and Busch 18 seconds back in eighth in what turned into a two-car struggle. Busch pitted the next time around to stay on the same strategy, but Truex stayed out to win his seventh stage of the season. However, Watkins Glen is not of those tracks considering they are seeing over 100,000 fans come through the gates, each and every year. "I love coming to these road courses". I won my first Cup race at a road course in Riverside. All three of Truex's road course wins were won with strategy, including last year at The Glen and this year at Sonoma in California's wine country. The Glen has had only one repeat victor - Marcos Ambrose in 2011-12 - in the past 12 years.
Sunday will be a marathon for NASCAR and the teams because inspection this week was moved to prior to the race.
Denny Hamlin started the race from the pole of the 220.5-mile event but lost the lead on Lap 2 when he was passed by teammate Busch in the sweeping Carousel turn.
Busch's shot at the win ended when his team failed to give him a full load of fuel during a yellow flag pit stop with 37 laps to go. NASCAR returns to the Irish Hills of Michigan next weekend for the Consumer's Energy 400, at Michigan International Speedway. 20 Toyota for Joe Gibbs Racing.
The news caught Cup series leader Kyle Busch by surprise after qualifying Saturday evening.More news: China defends Iran business ties after Trump threat
Elliott's win is a feel-good story that has a lot of angles. Justin Allgaier was third, followed by Justin Haley and Aric Almirola.
The cars of Paul Menard, who qualified 14th, and Kurt Busch, who qualified 21st, were the only ones to fail inspection.
Elliott hasn't competed in any of NASCAR's national series since he drove in the July Cup race at Daytona in 2012.
NASCAR Xfinity Series qualifying, MBCSN, 11:35 a.m. "That's key. It's impossible. when you get the vehicle out of the hauler to make that 20th-place auto a winning race auto by the end of second practice".
Chase Elliott (9) makes his way through the esses during a NASCAR Cup Series auto race, Sunday, Aug. 5, 2018, in Watkins Glen, N.Y.More news: Samsung starts producing high-capacity 4-bit SSD