The PGA Tour said that the former world number one had signed at the end of the second round for a three on the par-three fourth hole when he had made a four.
Spieth's disqualification was his first in 263 tournaments played on the PGA Tour.
"Today, I signed for an incorrect scorecard and stepped out of the scoring area, after thinking I went through all procedures to make sure it was correct," the 30-year-old wrote on X, formerly Twitter.
"Rules are rules, and I take full responsibility.
"I love this tournament and golf course as much as any on the PGA Tour so it hurts to not have a run at the weekend."
Tiger Woods will also be missing from the final two rounds of the tournament after the 15-time major champion withdrew on Friday due to illness.
