Bowman, one of five drivers already in backups for the Cup race, struck a wall coming out of a turn in Saturday's practice. Bowman was already in a backup Chevrolet after blowing the drive train in his main car during qualifying Friday.
"We don't have an issue. We've had a run of bad luck -- extremely bad luck," said Jeff Andrews, vice president of competition for Hendrick Motorsports.
Andrews gave an update in the garage as crews worked to switch Johnson's car into one for Bowman, and Andrews said the car will be fine for Bowman on Sunday. Bowman won his first career Cup race three weeks ago at Chicago.
"It is pretty rare," Andrews said of having to replace a backup car the day before a race.
"I've been here quite a few times and never hit the fence, especially there, but it just caught me off guard," Newman said.
Meanwhile, points leader Joey Logano will be starting eighth in his Team Penske Ford as he goes for his third victory at New Hampshire, which he calls his "home track."
Logano, from Middletown, Connecticut, said New Hampshire is the first place he saw a Cup Series race and that he loves racing in front of New England fans.
"There's nothing like winning at your home track, so you really want to make it happen there," Logano said.
Logano has won twice at New Hampshire and finished in the top 10 the past two races here.
"I enjoy the challenge of it. It's definitely one of the most technical race tracks that we go to. You have to be so precise about where you place your car," he said. "It's very flat. Cars don't do what you want them to do at all as flat as it is -- trying to get the car to turn and trying to get it to accelerate is always a tough thing, and there's a lot of variables."
Ryan Blaney's Ford had the fastest lap in Saturday's final practice session, averaging 133.572 mph. Toyota drivers had the two next-fastest times, with Hamlin -- in his backup -- averaging 133.226 mph and Kyle Busch at 132.739 mph.
Brad Keselowski, who clinched the pole in qualifying Friday, was sixth-fastest at 132.591 mph. Keselowski will be starting from the pole for the first time in nearly two years as he tries to win at New Hampshire for the first time since 2014.