The incident helped fuel the "Black Lives Matter" movement in response to multiple incidents of white police killing unarmed black men across the United States.
The officer, Daniel Pantaleo, was suspended earlier this month after a departmental judge ruled that the officer should be fired. He had previously been on desk duty since he was seen in widely viewed cellphone videos using a banned chokehold on Garner on a Staten Island sidewalk during an attempted arrest.
Police believed Garner was selling loose, untaxed cigarettes.
Commissioner James O'Neill said he struggled with the decision, which he made in recent days, after considering how Garner resisted arrest and, in his view, Pantaleo acted properly up until the moment he applied the chokehold after the two men fell to the ground.
O'Neill repeatedly returned to the empathy he had for Pantaleo, having himself been a uniformed officer for 34 years. "That could possibly be me," he said.
He also said he understood some police officers would be angry with him for not supporting one of their own.
"I've been a cop a long time, and if I was still a cop, I'd probably be mad at me, I would, for not looking out for us," he said.
But in the end, O'Neill said, he could not overlook that Pantaleo applied the chokehold despite having received sufficient police training that such a hold was barred, resulting in what he called a tragedy.
Garner's repeated dying cries of "I can't breathe," widely viewed on social media, became a rallying cry for the Black Lives Matter movement, which protests what its leaders call the disparate use of excessive force against black people across the United States.
His death, and the slow-moving investigations that followed, have generated some of the harshest criticisms of Mayor Bill de Blasio during his tenure and have spilled over into his campaign for the Democratic presidential nomination.
The case tested the liberal mayor's relationships with both civil rights activists, who have long complained that the city's black and Latino residents are harassed by police, and the rank-and-file police officers who work for him, some of whom say they have been made scapegoats by his office.
Firing was one of the few punishments still available. A Staten Island grand jury declined to indict Pantaleo in 2014 on criminal charges, and federal prosecutors said last month they would not bring charges because there was insufficient evidence.In 2015, New York City paid a $5.9 million settlement to Garner's family to avoid a civil lawsuit.