Darnold will be out indefinitely, hoping a team-prescribed throwing regimen will allow him to get back on the field in the coming weeks, perhaps as soon as Week 12.
"I think it's a smart decision not to play," Darnold said Monday. "I think, giving it thought, it just has to heal. It's got to have time. That's kind of our mindset."
The news is particularly troubling for the Jets (0-9) because they had hoped Darnold would be healthy enough to start after resting over the bye week.
The organization appears to be taking a more conservative approach than it did after the initial injury, a sprained AC joint, which occurred Oct. 1 against the Denver Broncos.
After sitting out two games, Darnold returned to the lineup with the idea that he'd manage the pain, with both him and team saying there was minimal risk. But he aggravated the shoulder late in a Nov. 1 blowout loss to the Kansas City Chiefs, and he hasn't played since.
The plan was for him to play Nov. 9 against the New England Patriots, but Darnold pulled himself out of practice Nov. 6 after a few throws, complaining of discomfort.
It certainly raises the question of whether he came back too soon. Darnold disputed that notion, saying, "With everything the doctors told me, I thought it was a good decision to come back."
He said his one regret was not sliding to avoid contact on a scramble against the Chiefs.
"I'm very confident that I'll play this year," Darnold said. "It's making sure that, when I do come back, I'm 100%, so that when I land on it or get hit, it's not getting reinjured."
Darnold already has begun an interval throwing program that will focus on volume and depth of throws. He started last week as he continued to rehab his shoulder.
Injured reserve isn't a consideration at this point, according to coach Adam Gase.
"We want to make sure he's in a good place the next time he steps on the field to practice," Gase said.
Gase said the hope is that Darnold can return sooner than later, but he was noncommittal about Week 12. The timing of the setback is bad for the Jets, who could face a huge quarterback decision after the season.
There's a good chance they will have the first or second pick in the 2021 draft, and the presumptive top prospects are Trevor Lawrence and Justin Fields, both quarterbacks. General manager Joe Douglas recently gave Darnold a vote of confidence, but the third-year quarterback is struggling.
The No. 3 pick in 2018, Darnold is 11-21 as a starter, and his QBR (44.7) over that span is 36th out of 36 qualifying quarterbacks.
Also on Monday, the Jets claimed offensive lineman Pat Elflein on waivers from the Minnesota Vikings. Elflein, a 2017 third-round pick who has started 42 games, was released Saturday after being activated from injured reserve. He suffered a thumb injury in practice before Week 2. He can play both guard positions and center.