Kymell Oram died on March 28, said Grace Burgess, a spokeswoman for the agency. Medical examiners have ruled his death a homicide, she said.
Oram, who was also known by his official name, Louis Mosley, was hospitalized on March 17 with blunt force injuries, cuts, broken ribs and damage to his lungs.
Paramedics found the boy unconscious in a Brooklyn home after responding to a 911 call.
Prosecutors say the boy was severely beaten by his foster mother's 19-year-old boyfriend while she was away from the house.
Kysheen Oliver, 19, was previously arraigned on charges including assault and reckless endangerment. They may now be upgraded.
Police say the mother left the boy in Oliver's care while she took two older children to school.
No decision had been made on whether to charge the foster mother, 35-year-old Teyuana Cummings.
The city's Administration for Children's Services has asked the Family Court to place the other two children into the agency's protective custody.
New York's child protection system has come under fire since the September death of another child, 4-year-old Marchella Pierce.
Pierce was beaten and drugged, and when she died she weighed only 18 pounds, half the normal weight of a 4-year-old.
On March 23 a grand jury indicted an investigator and supervisor at the Administration for Children's Services on charges of negligent homicide. Prosecutors say the two workers falsified information about inspection visits to Pierce's home. The workers say they simply didn't enter the information into computers until later because they were too busy.