"It was pretty cool to see the 2, the 11 and the 48 running 1-2-3 through a large portion of the night," Johnson said.
But it was Bowyer in Victory Lane at the end, for the third time this season in his first year with Michael Waltrip Racing and manufacturer Toyota, a partnership that's working out far better than expected.
"Who thought in a million years I'd walk into the situation I've walked into?" he asked in Victory Lane.
The race was the first since 1979 without an Earnhardt as Dale Earnhardt Jr. sat out with a concussion. The announcement was made Thursday after Earnhardt sought medical attention for a lingering headache from the 25-car accident Sunday at Talladega.
His doctor said he also sustained a concussion in an Aug. 29 crash at Kansas.
Regan Smith got the start for Earnhardt, but it was short-lived. The engine in the No. 88 Chevrolet failed during the first third of the race, sending Smith to the garage for the night.
Smith is scheduled to be back in the car next week at Kansas, which has two open days of testing and gives Smith more time to get acclimated with the Hendrick Motorsports crew.
"It's a good team, it's a good car and everybody at Hendrick Motorsports does a great job," Smith said. "I'm looking forward to next week. I'm getting comfortable with the cars, comfortable with the equipment. Should be fun to go to Kansas."
Kurt Busch, who was hired to replace Smith at Furniture Row Racing next season, got a jump on that job early by taking over the job this week and finished 21st in his debut race. That opened up Busch's seat at Phoenix Racing, and Smith was scheduled to drive that car at Charlotte.
But when Smith got the call to replace Earnhardt, the team gave a chance to AJ Allmendinger, who made his first start since his July suspension for failing a random drug test. Allmendinger, who had not raced since June 29, finished 24th.
Greg Biffle, who set a track record in winning the pole, finished fourth. It moved him up three spots in the points to sixth. He was followed in the finishing order by non-Chase drivers Kyle Busch, Mark Martin and Carl Edwards.
Kasey Kahne was eighth, but it cost him a spot in the Chase standings and he's now fifth. Joey Logano, winner of Friday night's Nationwide race, was ninth and Chase driver Martin Truex Jr. was 10th to give MWR all three of its drivers in the top 10.