Prosecutors say he was armed, although no weapon is visible in his hands in the video when he is struck.
Tensions over racism and policing are already high in the United States as nearby Minneapolis hosts the trial of a white former policeman charged with murdering African American George Floyd in the same week that the fatal police shooting of an unarmed Black motorist sparked violent protests in a suburb of the city.
In a news conference Thursday ahead of the latest video's release, Chicago Mayor Lori Lightfoot called for a peaceful response from residents, describing the footage as "excruciating to watch".
Ms Lightfoot would not comment on whether Toledo - who was laid to rest on Friday last week - was holding a gun when he was killed, despite saying repeatedly earlier in the week that he was.
"I don't think it matters whether Adam is a choir boy, whether he is involved in some other untoward activity - the fact of the matter is that he was walking in the street and he was shot unarmed," Adeena Weiss-Ortiz, the Toledo family lawyer, told reporters.
Toledo, who reportedly has American Samoan heritage, was laid to rest last week.
The Civilian Office of Police Accountability is reviewing footage from body cameras worn by the responding officers and other video, along with audio recordings from surveillance sensors.
'Drop it, drop it'
Police responded to a report of shots fired at 2: 30 am on the Midwestern city's predominantly Latino and Black West Side. They chased Toledo and 21-year-old Ruben Roman - who had fired the originally reported shots, according to prosecutors - on foot.
Mr Roman was quickly apprehended as the pair fled down an alley and the body cam footage shows an officer cornering Toledo. Prosecutors say the boy was armed, although no gun can be seen in the footage as Toledo raises his hands.
"The officer tells (Toledo) to drop it... as (Toledo) turns toward the officer," Cook County assistant state's lawyer James Murphy said Saturday in a bond hearing for Roman.
"(Toledo) has a gun in his right hand. The officer fires one shot at (Toledo), striking him in the chest," Mr Murphy said.
The gun Toledo was allegedly holding, a Ruger 9mm, landed against a nearby fence, Mr Murphy said, and the officer immediately rendered aid - but the 13-year-old was pronounced dead at the scene.
There was gunshot residue in the youngster's right hand, and shell casings that were found where Roman had allegedly been firing the weapon matched the Ruger, Mr Murphy added.
Prosecutors have not indicated the point at which they say the gun ended up with Toledo.
On Thursday, Chicago network WGNTV reported that the Cook County state's attorney's office said prosecutor Mr Murphy was in fact "not fully informed."
"An attorney who works in this office failed to fully inform himself before speaking in court," Sarah Sinovic, a spokeswoman for Cook County State's Attorney Kim Foxx, told WGN Investigates Thursday.