Reynaldo Cuevas, 20, and his uncle were in Natalie Grocery, at 1229 Franklin Avenue, when armed robbers burst in as the store was closing at 2 a.m., police sources said.
The victims were held hostage, but managed to escape just as police were arriving, the victim's cousin told the Daily News.
As they sprinted from the store, Cuevas was shot in the torso by a cop, police sources and a witness said.
"The first guy ran out with his hands on his head," said Jesse Rodriguez, 23, a neighborhood resident, of one of the victims.
"The second guy ran out and tripped by the fire hydrant," he added, referring to Cuevas. "And the cops shot him."
Cuevas, who was not armed, was shot once in the torso, police and witnesses said.
"People were screaming, 'He works there! He's an employee!" Rodriguez added. "He was innocent."
Cuevas was taken to St. Barnabas Hospital where he was pronounced dead.
The circumstances of the shooting were still under investigation, police said.
Police sources said the cop who fired the shot believed Cuevas was a suspect chasing the first victim.
Cops made more than one arrest, police said, but did not provide further details.
Meanwhile, a marked police vehicle racing to the scene got into an accident, an NYPD spokeswoman said. An officer inside the car was injured and taken to a local hospital, she said, but was not seriously hurt.
Rodriguez said he spoke to Cuevas just four hours before the shooting.
"We were just talking about life, music, sports, baseball," he said. "He was a Yankees fan."
Alfredo Lambert, 27, remembered Cuevas as a hard worker who valued the bodega's customers.
"He treated everyone with respect," Lambert, a computer technician, said. "He was our little angel."