Daniel Penny, a former Marine who choked a fellow subway rider on an uptown F train last year, was acquitted on a charge of criminally negligent homicide on Monday, ending a case that had come to exemplify New York City’s post-pandemic struggles.

The jurors decided that Mr. Penny’s actions were not criminal when he held the rider, Jordan Neely, in a chokehold as the two men struggled on the floor of a subway car on May 1, 2023. Mr. Neely, who was homeless and had a history of mental illness, had strode through the subway car that afternoon, yelling at passengers and frightening them, according to witnesses.

After the forewoman read the verdict, those in the courtroom erupted in responses, some cheering. Mr. Neely’s father, Andre Zachery, and his lawyer were asked to leave the room.

The jurors had spent about three days trying to come to a unanimous decision on whether Mr. Penny, 26, was guilty of manslaughter — a higher charge — in the death of Mr. Neely, 30. On Friday, the jurors sent two notes to the judge overseeing the trial saying that they had deadlocked.

After the jurors — seven women and five men — sent the first note that morning, the judge, Maxwell T. Wiley, instructed them to resume their deliberations. When the jurors sent the second note in the afternoon, telling Justice Wiley that they were still unable to reach an agreement, he granted the prosecution’s request to dismiss the charge. He sent the jurors home for the weekend, telling them to prepare to begin deliberating on the second charge on Monday. Ultimately, they decided to acquit Mr. Penny.

The decision was a defeat for the office of Alvin L. Bragg, Manhattan’s district attorney. Earlier this year, Mr. Bragg, a Democrat, successfully prosecuted President-elect Donald J. Trump, securing a conviction against him on 34 felony counts of falsifying business records.