His participation in Thursday's PGA Championship in Kentucky, the final major of the year, must be highly doubtful although Woods said it was too early to speculate.
He also must be considered increasingly unlikely to be on the American team for next month's Ryder Cup in Scotland.
He looked to be in pain after his drive at the ninth hole of the final round before deciding to retire on four over par, 18 shots behind overnight leader Sergio Garcia at Firestone Country Club.
Woods, who had made a double-bogey on the seventh hole, was limping as he climbed into a golf cart and left the course. He later issued a short statement.
"It happened on the second hole when I hit my second shot. I fell back in the bunker. I just jarred it and it's been spasming ever since," he said.
"It's just the whole lower back. I don't know what happened when I landed."
The latest injury setback comes barely four months after Woods had lower back surgery to relieve an impinged nerve.
He had the procedure after intense pain caused him to pull out of the Honda Classic on March 2, also during the final round.
The 38-year-old missed the first two majors of the year, the Masters and U.S. Open, and the Bridgestone Invitational was just his third event since he returned to action.
He has long been driven by a burning desire to surpass the record of 18 major titles held by Jack Nicklaus.
But he has not won a major since the 2008 U.S. Open, and has reached an age after which nobody in the modern era has regularly won major championships, even fully healthy.
Even before his latest setback he struggled to drive the ball as well as the current crop of top players such as Rory McIlroy, Adam Scott and Garcia.
Woods showed no immediate sign of distress after hitting his second shot from an awkward lie in lush rough above a bunker at the par-five second hole on Sunday.
He lost his balance after playing the shot but stayed on his feet as he trotted eight paces through the sand back to the fairway.
But he was in obvious pain by the fifth hole, where he winced in pain after his tee shot.
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