He became just the second player in the past four years to fail to reach the weekend after holding a piece of the opening-round lead.
"I've never led a tournament and missed the cut before," Spieth said.
"Just a bad day."
Chris Kirk, another of the first-round co-leaders, holds a one-shot advantage at the tournament's midpoint.
Kirk shot a five-under-par 65 in the second round at Waialae Country Club, leaving him at 11-under 129.
Adam Scott is the best-placed Australian, six shots behind Kirk after a four-under 66.
The third first-round co-leader, Taylor Montgomery, is tied for second with JJ Spaun at 10 under.
Montgomery carded a 66 on Friday, and Spaun moved up with a 64, though he bogeyed his final hole when he had a chance to match Kirk for the overnight advantage.
Spieth, who opened with a 64, produced a 75 in the second round. He had one bogey and one birdie through his first four holes on Friday, then was doomed by a stretch of four consecutive bogeys on either side of the turn.
Spieth added one more bogey at No.15 and couldn't make up any ground the rest of the way, finishing one stroke below the cut line.
"It was a weird, weird day," Spieth said.
"Didn't feel like it was much different. Felt like I had a really bad deck of cards today. Made a couple ... bad swings from off the tee. Other than that, I didn't play that different."
6°C