"Jason has a strained ligament in his lower right back with muscle spasm," his management company said in a statement shortly after early departure at East Lake.
"He withdrew as a precautionary measure. Jason should be fine with some rest after a long break in the offseason."
There was no immediate word on whether he still planned to compete in two tournaments in his homeland in November - the Australian Open in Sydney and World Cup of golf in Melbourne.
Despite the reassuring statement, Day's injury is hardly good news for a player who has been plagued with injuries and illnesses throughout his career.
On Wednesday, Day said his back was an on-going problem that flared up occasionally.
"I had a bulged disc in 2014," he told reporters. "Through the exercise that I've been doing, that bulged disc ... has actually come in, which is kind of a miracle because ... you're thinking that it's either going to stay the same or get worse.
"Unfortunately, I've got an annulus tear in my disc, annulus tear of the ligament. I've torn it once before, and I've retorn it again."
He also said after Thursday's opening round that he had felt pain on a few shots, but not constantly.
"There was a couple of drives out there where ... felt a bit of a sharp pain in my back," he said after the round.
Day's withdrawal eliminates him from contention to claim the $10 million bonus awarded this week to the winner of the PGA Tour's season-long FedExCup points race.
Day's early departure at the Tour Championship came after he launched two full-throttled lashes with his driver at the par-four eighth.
He pulled his drive into the lake left of the fairway, took a penalty drop in the rough and then took another mighty swing with the driver and sprayed the ball into more rough.
He did not appear to flinch after either shot but after walking up to his ball right of the green, he decided to call it a day.
He shook hands with playing competitor Kim Si-woo and trudged back to the clubhouse.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Larry Fine)
