Mickelson, who birdied his final hole on Friday to make the cut, exited after 10 holes at TPC San Antonio. He was two over par for the round and five over for the tournament, well off the pace of leader Steven Bowditch, who held a three-shot lead at 12 under after the third round.
The PGA Tour broke the news via Twitter that Mickelson was done for the day.
Mickelson later released a statement saying he sustained the injury teeing off at No. 1, which was his 10th hole of the day.
“I pulled a muscle on my downswing trying to hit it hard,” Mickelson said a statement. “It just killed and it wouldn't subside for 10 or 12 seconds. I'm going back to San Diego (for) a couple of days and have a doctor look at it, but there's really not much you can do for a pulled muscle. I hope I'll be OK to play the Shell in Houston, but I just don't know.”
Mickelson had told reporters on Friday that all was well.
"I’m hitting the ball hard," Mickelson told reporters Friday. "I’m hitting it high, my speed is back, my back feels great, my body feels great, and I’m able to hit the ball hard again."
Mickelson withdrew earlier this year from the Farmers Insurance Open at Torrey Pines because of a back injury, and Tiger Woods is a question mark for the Masters in early April because of recurring back problems.
Now eyes will turn to next week's Shell Houston Open, which Mickelson has entered and which he won in 2011.