His next effort failed to reach the hole and his third putt - his sixth shot - then rattled nearly seven feet past the target, with Lee's following attempt finishing just under four feet from the cup.
The world No 108 saw his eighth shot go further past the target than any of his previous efforts, before eventually holing from seven feet seven inches - the longest putt of the lot - to finish his round with a quintuple-bogey nine.
The six-putt from four feet saw Lee close out an eight-over 78.
According to Golfweek, Lee withdrew due to a wrist injury.
Lee last withdrew from a tournament in 2017, when he pulled out of the BMW Championship near Chicago after just two holes citing a lower-back complaint following a birdie and a bogey.
Yesterday fellow Kiwi Ryan Fox missed the cut after carding a 15-over 85 in his second round. Just three players are under the card for the tournament heading into the final round.
21-year-old Matthew Wolff leads the way with a two-shot lead over Bryson DeChambeau
after recording a five-under 65 today. Wolff is appearing in just his second major after an impressive tied for fourth at the PGA Championship last month.
DeChambeau, three-under, and South African Louis Oosthuizen at one-under, are the only other two players under the card after three rounds. Japan's Hideki Matsuyama and American duo Xander Schauffele and Harris English are all at even-par, five shots back from Wolff.
Wolff has only one PGA Tour victory to his name after making his debut on the tour last year. That came at the 3M Open where he beat DeChambeau and Collin Morikawa by one stroke after an eagle on the 72nd hole.
Wolff hit only two fairways today on a course — and a major — with a blueprint for avoiding the rough. The only number that mattered to the 21-year-old Californian was a two-shot lead going into the final round.
"There's a lot of holes out there that maybe people would try to hit it in the fairway or maybe take the safe play because it is a U.S. Open, and they know that pars are a good score," Wolff said. "But I don't really like to think of it that way. I like to go out there and do what I feel comfortable with, rip dog and see how it goes from there."
It's going so well that Wolff is one round away from becoming the youngest U.S. Open champion since Bobby Jones in 1923.
Whether it was the first cut or the nasty rough, Wolff kept giving those hips one last swivel before blasting away and giving himself birdie chances. He shot 30 on the front nine — and missed a 6-foot birdie putt on No. 8 after hitting his first fairway of the round — and then let so many others fall apart.
Patrick Reed, tied for the lead at the turn, couldn't find the fairway and paid dearly with a 43 on the back nine. Reed had a three-shot lead after two holes. He walked off the 18th green with a 77 and was eight shots behind.
"Anyone in my position would be frustrated, especially with having the lead going into today," Reed said. "The great thing is there's always tomorrow, and like I said, it's a U.S. Open. Even though eight shots seems like a lot ... you never know."
Collin Morikawa won the PGA Championship last month in his first try at age 23. Now here comes Wolff, playing his first U.S. Open at age 21. Is he next?
The last U.S. Open champion to win in his debut was Francis Ouimet in 1913. That also was the last time the U.S. Open was played in September.
"I'm probably going to be a little antsy. It's the U.S. Open, and I have a lead," Wolff said. "I'm going to try to keep my nerves as calm as they can be. I put myself in a really good spot. I did everything that I could do up until this point, and tomorrow I'm going to go out there, I promise you I'm going to try my best."