The American was eight holes into his final round at the Firestone Country Club when he appeared to feel discomfort following his tee shot at the par-four ninth.
Woods had earlier grimaced after playing a bunker shot at the second, with the 38-year-old later confirming that he had hurt his back.
"I just jarred it, and it's been spasming ever since," Woods told a PGA Tour official before leaving, as reported by the PGA Tour's official website.
"It's just the whole lower back," he added. "I don't know what happened."
After being driven off the course in a golf buggy from the ninth tee box, tournament organisers revealed Woods would not be continuing his round.
While the extent of the problem has yet to be confirmed, the injury is a potentially serious setback for the former world number one, who has only just returned following a previous back injury.
Woods underwent surgery in March to alleviate the effects of a pinched nerve and was forced off the tour for almost three months - including missing the Masters for the first time in his career.
The World Golf Championships Bridgestone Invitational had marked only his third tournament since his return.
His latest fitness worry now looks almost certain to rule him out of next week's US PGA Championship, the final major of the season, while it could also put in further jeopardy his hopes of featuring in next month's Ryder Cup at Gleneagles, with the biennial tournament due to begin on September 26.
Woods had already faced a battle to qualify automatically for the US team, and had begun the Bridgestone Invitational knowing that only a strong showing at Firestone, as well in the US PGA, would guarantee him a spot in Tom Watson's line-up.
He would likely have been a strong option for a captain's wildcard pick regardless, despite a mixed Ryder Cup record of just 14 1/2 points in 33 matches played, but his hopes now appear to be hanging in the balance.
Some pundits have even expressed concerns over his wider future.
Woods was four over par after eight holes of his final round at Firestone, a venue at which he has won eight times in the past - including claiming the title by seven strokes in 2013.
