Camacho was pronounced dead after being taken off life support following a second heart attack early Saturday morning, Rio Piedras Medical Director Ernesto Torres said.
Puerto Rico officials planned a public wake for the boxer at the Department of Sports & Recreation headquarters in San Juan, but details were pending.
The former U.S. boxing champ had been declared brain dead on Thursday after he was shot on Tuesday while sitting in a car with a friend, Adrian Mojica Moreno, 49, outside a liquor store in the San Juan suburb of Bayamon, Camacho's birthplace.
Two gunmen opened fire on the car, killing the driver, Mojica Moreno, and hitting Camacho in the jaw. The bullet fractured two vertebrae and lodged in his shoulder, damaging the arteries that carried blood to the brain, doctors said.
Police found nine small bags of cocaine in the driver's pockets and one open in the car.
The shooting is under investigation and no arrests have been made.
Camacho, a left-handed fighter who grew up in New York's Spanish Harlem neighborhood, had a record of 79-6-3 with 38 knockouts. His three-decade career featured fights with a "who's who" of boxing and a flamboyant style that included entering the ring in an outfit based on the Puerto Rican flag.
Camacho's body was taken to the hospital's pathology section and brought to the Institute of Forensic Sciences as required by law, Torres told reporters.
El Nuevo Dia newspaper reported the family planned a funeral in New York, where Camacho grew up.
Family members had debated removing him from life support, with some members including his son Hector "Machito" Camacho holding out hope for his recovery.
On Friday evening, his mother Maria Matias acknowledged during a brief talk with reporters at the medical center that that "God has taken him" and indicated that she was waiting for the arrival of Camacho's other children to Puerto Rico before disconnecting him.
Some family members had discussed organ donation, but Torres said too much time had passed from when the former fighter was declared brain dead on Thursday morning to donate his organs now.
Camacho Jr. lamented the crime and violence confronting Puerto Rico. "You have to stop the violence and the drugs. Rap singers have to stop glorifying violence. This is for the youth. All the street promises them now is death, drugs, and jail."