The final major tournament of the year tees off in four days at Valhalla Golf Club in Louisville, Kentucky, and Woods was hopeful it might signal a return to form as the 14-time major champion chases the career record of 18 majors won by Jack Nicklaus.
Woods, 38, underwent back surgery March 31 to relieve pressure on a pinched nerve and this was only this third event since the operation.
He apparently injured his back again when he hit his second shot at the second hole from an awkward stance and fell backward into a bunker.
"I just jarred it and it has been spasming ever since," Woods said. "It's just the whole lower back."
Woods missed the cut at the PGA event he hosts in Washington in late June and finished level 69th at the British Open last month, his worst 72-hole showing in a major as a professional but his only four-round effort without pain since February.
Woods struggled to finish the round even after his injury but was 65 yards short on a par-3 hole and found a concession stand with an approach shot.
As he departed, Woods said his pain became progressively worse in the last round of his final PGA Championship warm-up event at Firestone Country Club -- a course where he has won eight times.
At the time he withdrew, he was three-over par for the final round and stood four-over for the tournament.
"After grimacing in pain after his tee shot on No. 9, Tiger Woods has withdrawn from the @WGC_Bridgestone," tweeted the PGA Tour.
Woods was seen holding his back as he departed, being driven off the course in a golf buggy, forced to sit ramrod straight to help alleviate the pain.
- Debilitating injury -
Woods' playing partner, Masters champion Bubba Watson, said he didn't actually see that shot on which Woods "tweaked" his back.
"I didn't see it because I was watching his ball, but he said he jumped back in the bunker, fell in the bunker," Watson said. "Then hitting it out of the rough a few times is just going to make the strain on the back even worse.
"Hopefully he recovers and he gets ready for next week," Watson said.
In talking about the pinched nerve, Woods has called it the most debilitating injury he has faced, one that kept him bed ridden for days and unable to do even the most basic of tasks.
Woods spoke at Washington about how he felt he was ahead of schedule and at the very early edge for what doctors had said might be his timetable for healing, although the latest flare of back pain indicates he might have pushed himself too far too fast to return in time for the British Open and PGA.
The back pain likely dooms his slim chance at qualifying for the US Ryder Cup team on points and probably means US Ryder Cup captain Tom Watson would not risk a captain's pick on him given the potential health risk as he assembles a squad to try and win back the trophy in September at Gleneagles in Scotland.