Johnson suffered a lower back injury on Wednesday when he slipped and fell down a set of stairs at a rented home. Care and treatment plus some last-minute therapy was not enough to get him fit enough to swing without soreness when he contacted the ball.
That led to Johnson walking off the first tee as his planned playing partners, two-time Masters champion Bubba Watson and 2016 PGA Championship winner Jimmy Walker, started in the day's final group.
"We talked to him," Watson said. "I was on the training table the same time he was on the training table before we hit balls, so I saw him before we went out there.
"You want him to be healthy, you know? And so for us we knew if he doesn't play we're going to have a slow day. We're not thinking about him playing or not. We just want him healthy. We want him strong. You don't want to wish that on anybody."
Jordan Spieth, the 2015 Masters champion and a friend of Johnson, watched as Johnson's name was removed from the manually operated Augusta National scoreboards and guessed he had withdrawn.
"Certainly really unfortunate. And as a friend of his and somebody who has played a lot of golf with him, I know this it must really, really not be good in order for him not to tee it up," Spieth said.
"And I certainly wish him well."
Five-time major winner Phil Mickelson, who would become the oldest Masters champion at 46 if he wins a fourth green jacket Sunday, did not learn about Johnson until he was almost done.
"I just found out on 18 green that he didn't start and, gosh, he's been playing some great golf," Mickelson said. "I know it's disappointing."
Australia's Adam Scott, the 2013 Masters champion, was hopeful for a quick return by Johnson, who won his three prior starts to become the Masters favorite with oddsmakers when the week began.
"That's really sad," Scott said of Johnson's withdrawal. "I can't imagine having to do that. It's disappointing, for sure, for everybody.
"The way he has been going, a freak accident, he's obviously very, very injured, because to pull out of the Masters when you're in the kind of form he's in, it must be a very difficult decision to make."