His Furniture Row Racing No. 78 Toyota led 25 laps in that race before the engine blew.
With his famous father, Hall of Famer Bill Elliott spotting from above, Chase maintained his slim advantage as Truex tried to find a way by.
Joey Logano, who won the Zippo 200 Xfinity race moments earlier, qualified sixth.
Midway through the segment, the Big 3 were running in the top 10, but Elliott dominated and beat Busch by 1.3 seconds. Busch pitted the next time around to stay on the same strategy, but Truex stayed out to win his seventh stage of the season.
Truex did come close to passing Elliott on the last lap.
It promised to turn into a fuel mileage race as the laps wound down, and nobody has been better with the strategy than Truex and crew chief Cole Pearn. When Truex bobbled in the chicane on the final lap, Elliott was home free. He won at Sonoma, California, the only other true road course on the regular-season schedule, in late June and is the defending Watkins Glen victor. "If you can win on speed, you try to win on speed".
When Chase Elliott ran out of fuel on his victory lap on Sunday at Watkins Glen, seven-time champion Jimmie Johnson helped push him back to the finish line to celebrate with his team. He put his auto exactly where I needed mine to be. On race day, the big three were looking like the best of the field once again, but the #9 Sun Energy1 vehicle of Chase Elliott was a man on a mission.
The trio was as dominant as always last week at Pocono when Busch and Harvick had to start at the back of the field after their cars failed postqualifying inspection.
Catching up has been an uphill battle, even for drivers under the same roof. Elliott hasn't made a NASCAR national series start since the 2012 Firecracker 400 at Daytona International Speedway. "That doesn't happen because everybody is improving and you can not improve that much".
No inclement weather is expected Sunday, but there's still a wrinkle to the proceedings already because instead of NASCAR announcing a field and then having to change it after handing out inspection violations, the Watkins Glen inspections are only taking place Sunday morning. "That's cool", Busch said.
Logano held off a challenge from Keselowski to win the Zippo 200.
Racing announced Saturday on Twitter after the Xfinity Series race at Watkins Glen that the 62-year-old Elliott will drive the No. 23 Chevrolet at Road America in Wisconsin on August 25.
Logano started from the pole in the road race that was red-flagged for rain, forcing the drivers to briefly switch to rain tires. He won both the Xfinity and Cup races in 2015 and won the Xfinity race on Saturday. Justin Allgaier was third, followed by Justin Haley and Aric Almirola.
Keselowski spun out trying to pass Logano with under three laps to go and finished 10th.