Indoor dining will once again be barred in New York City restaurants starting on Monday, Gov. Andrew M. Cuomo said on Friday, in a significant reversal of the city’s reopening that comes as officials try to halt the escalation of a second wave of the coronavirus and avoid a broader shutdown.

The decision, which Mr. Cuomo earlier this week suggested was all but certain, is a crushing blow to the city’s restaurant industry, a vital economic pillar that has been struggling all year in the face of pandemic restrictions and a national recession.

Mr. Cuomo acknowledged the hardship his decision was likely to cause and once more called on federal lawmakers to provide relief to the hospitality industry. Congressional leaders have so far failed to reach an agreement on a new economic stimulus package.

Even as he announced the new restriction, the governor provided data that showed restaurants and bars were likely not the primary driver of new cases in the state, lagging far behind private gatherings.

Still, the governor portrayed the end of indoor dining in New York City as necessary given new federal guidance, an increasing rate of virus transmission and the city’s population density. Mr. Cuomo has warned that an anticipated surge in cases this winter threatens to overwhelm the medical system. Over the last month, while preparations have begun to distribute the first doses of a vaccine, virus-related hospitalizations in the state have more than tripled.

The governor said on Friday that the city was currently on a trajectory to hit 90 percent of its hospital capacity, at which point he would close down all nonessential businesses. He described the prohibition on indoor dining as an attempt to avoid such a move.

Restaurants and bars, Mr. Cuomo said, are “one of the few areas that we think we can actually make a difference.”

The order came as the 21 Club in Manhattan appeared to become the latest iconic New York City restaurant to succumb to the pandemic. In a notice filed Wednesday with the state’s labor department, the restaurant — a favorite of President Trump — said it would “indefinitely” cease its operations and lay off all of its employees next March.

In a statement, the restaurant’s owners said that the pandemic, and an anticipated long recovery, made it unfeasible to reopen the 21 Club “in its current form for the foreseeable future.” But the owners said they hope to reopen at some point, and are exploring long-term options, according to the statement.

The restaurant, which opened as a speakeasy during prohibition, first closed and laid off employees on March 16, when the governor ordered nonessential businesses in the state to shut down. Though officials eventually permitted outdoor dining and limited indoor dining, the 21 Club remained closed to customers.

Bill Granfield, the president of Local 100 of Unite Here, the union representing the restaurant’s workers, said that the union was hopeful that the restaurant might one day reopen in some fashion, he said.

Andrew Rigie, the director of the New York City Hospitality Alliance, said in a statement that the governor’s decision “is at odds with the state’s own data that’s been presented as driving these decisions, and it will be the last straw for countless more restaurants and jobs.”

Mr. Rigie also called for more economic support for struggling restaurants and bars, saying the end of indoor dining would “severely jeopardize” their survival.

For months, New York City’s restaurant owners have warned that their businesses, many of which operate on tight margins in the best of times, are on the edge of financial collapse. Thousands of employees, many of them low-wage workers, have been laid off since March, and their jobs have yet to fully return.

The industry’s anxieties are only mounting as winter approaches and frigid temperatures threaten to deter customers from dining outdoors. Industry groups have called repeatedly for federal or state financial assistance, with restaurant and bar owners watching nervously as stimulus talks drag on in Washington.

The governor’s announcement came after weeks with shifting messages on indoor dining, which resumed in New York City only at the end of September.

As virus cases rose across the state this fall, Mr. Cuomo hesitated to impose the widespread restrictions that he implemented in March, when he limited restaurants and bars to takeout and delivery.

In October, the governor said he would shutter indoor dining only in the hardest-hit areas in the state, so-called microclusters. He briefly changed course in late November, saying he would shut down indoor dining citywide if the seven-day average test positivity rate hit 3 percent. He walked back that statement about a week later.

Mr. Cuomo and his aides have said that the state’s approach has changed to follow evolving guidance from epidemiologists. Until this week, the governor had focused much of his attention on parties and other indoor gatherings and had downplayed the risks of indoor dining, even as growing evidence suggested it was a significant source of the virus’s spread.

But on Monday, Mr. Cuomo had warned that he would curb indoor dining in regions where hospitalizations did not stabilize, citing recommendations from the Centers for Disease Control and Prevention that described eating at indoor restaurants as a “particularly high-risk” activity.

Then on Friday, Mr. Cuomo said that contact tracing data showed that restaurants and bars were the fifth main source of new infections in the state, well behind household and social gatherings. The data is based only on those who give a response to contact tracers and does not capture every infection in the state, officials have said.

Of 46,000 cases between September and November, 1.43 percent could be linked to restaurants and bars, compared to 73.84 percent connected to private gatherings and 7.81 percent tied to the health care system, the second-largest source.

The governor acknowledged the disparity but said the state was limited in how it could address such gatherings and other sources of infection.

“We’re doing everything we can,” he said.

Mr. Cuomo did not announce new restrictions on restaurants and bars in the rest of the state, which were allowed to reopen more quickly and have been operating at 50 percent maximum capacity indoors, compared to 25 percent in New York City.

However, he said the state would monitor hospitalization numbers over the weekend and “make any adjustments next week” if the data suggested it was necessary.

The governor also did not provide a timeline or threshold for indoor dining to resume in New York City. An adviser, Jim Malatras, said the state would monitor virus cases and hospitalizations over a two-week period to see if trends allowed for eating indoors to restart.

As of Friday, 1,668 people were hospitalized with the virus in New York City, Mr. Cuomo said. Statewide, 5,321 people were hospitalized. The rate of transmission in the state was estimated at 1.3, meaning that each infected person was estimated to infect 1.3 other people.

Luis Ferré-Sadurní contributed reporting.