Officer Brian Moore, 25, was in an unmarked car pursuing Demetrius Blackwell when he was gunned down in a middle-class residential neighborhood in the New York City borough of Queens, police said.
Blackwell, 35, who was wanted on a weapon charge, was arrested and charged with attempted murder.
Moore succumbed to his injuries on Monday.
Bratton told a press conference that the Queens district attorney would ask a grand jury to indict Blackwell on a charge of first-degree murder.
Moore is the first New York City officer killed in the line of duty since two uniformed officers were ambushed last December.
Moore and his partner had been trying to question Blackwell, who has an extensive criminal background, after they saw him seeming to adjust an object in his waistband, police said during a weekend news conference.
Police said Blackwell pulled out a gun and fired into the vehicle, striking Moore.
When he was arrested Blackwell was charged with first-degree attempted murder, assault and other counts and ordered held without bail.
Moore, who came from a family of police officers, joined the New York City Police Department in July 2010, according to Mayor Bill de Blasio. He lived in the suburban Long Island town of Massapequa.
Uniformed officers who had kept vigil outside Jamaica Hospital in Queens saluted as Moore's body was taken away in an ambulance.
"The people of this great city should take pause this afternoon just to recognize the life of a brave young man who took an oath 4-1/2 years ago to keep the people of this city safe," said Police Chief of Department James O'Neill, who worked with Moore's father on the police force.
"That's what he was doing when he was brutally murdered just a few short days ago," O'Neill said.
The mayor in a statement expressed his sympathies.
"Our hearts are heavy today," he said. "Brian served with distinction and he put his life on the line each day to keep us all safe."
Unlike the shooting in Brooklyn just days before Christmas of Officers Rafael Ramos and Wenjian Liu, who were targeted for their uniforms, Moore was in plainclothes and in an unmarked car, authorities said.
Police said Blackwell was wanted on outstanding charges, including grand larceny, criminal possession of a weapon and menacing. His arrests included two for assaulting police officers, the Daily News reported.
Two New York plainclothes officers were shot while responding to an armed robbery in the Bronx in January and survived their injuries.
