The commissioner also said he expected some NYPD officers would be upset with the decision, but emphasized the evidence agreed with a recommendation by NYPD administrative judge Rosemarie Maldonado that Pantaleo be fired.
Four officers attempted to arrest Garner, 43, on suspicion of illegally selling cigarettes on a sidewalk in Staten Island on July 17, 2014.
In a confrontation caught on video footage, Garner repeatedly tells officers that he was unwilling to be taken into custody, which prompted Pantaleo to bring him to the ground by his neck as the man said he could not breathe 11 times. The confrontation is caught on amateur video, including Garner's words "I can't breathe", which become a rallying cry among protesters. Pantaleo has remained employed, earning more than $100,000 a year, since the incident. A civil suit filed by Garner's family against the department was settled out of court in 2015 for $5.9 million in damages, however the family insisted "the victory will come when we get justice".
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 "an irreversible tragedy".
Federal prosecutors then said last month they would not bring charges.
"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.
Garner died just weeks before Michael Brown was fatally shot by a police officer in Ferguson, Missouri, and both cases sparked a national movement for police reform. After employing the fatal chokehold, Pantaleo and the other officers dragged Garner to the pavement.
Civil rights campaigner the Rev Al Sharpton said Mr Garner's family was "relieved but not celebratory".
"Justice has been done", de Blasio said.
Police Benevolent Association President Patrick Lynch wanted O'Neill to support Pantaleo and not fire him in order to allow officers "to be effective again".
Mr Garner's daughter Emerald Snipes-Garner wore a T-shirt with "MURDERER" emblazoned across the front.
Garner's mother, Gwen Carr, decried the decision not to pursue charges against Pantaleo during an emotional press conference last month.
"We're here with heavy hearts because the DOJ has failed us", she said.
Police Commissioner James O'Neill said he would make an announcement at 12:30 p.m. Monday on an undisclosed topic.
New York City's police commissioner has scheduled a midday news conference as the city waits for his decision on whether to fire a police officer involved in the 2014 death of an unarmed black man. "While July 17 is and always will be a somber day for the City of NY, today we can rest assured that Daniel Pantaleo will never patrol our streets again".