The 12-year old, Kanari Gentry-Bowers, was also shot Saturday and is now in critical condition at Stroger Hospital.
Lavontay White, identified by the Cook County Medical Examiner's office, was later pronounced dead in hospital.
In the front of the vehicle, Lavontay's pregnant, 20-year-old aunt and her boyfriend were hit. Devonte was later transported to a hospital in fair condition but both she and her unborn child will survive.
While Chicago police did not name the suspect in Tuesday's deadly shooting, Johnson did say that the department had promising leads and was tracking down the shooter and whoever else may have been in the vehicle when the fatal shots were fired. Investigators have "very optimistic leads" in the case, police said, adding that detectives are now analyzing surveillance video from the area.
The shooting of Lavontay White and a 26-year-old man were captured on Facebook Live by the woman who was also injured in Tuesday's attack.
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About 11:55 a.m., a 23-year-old man was fatally shot in the 2000 block of East 71st Street in the South Shore neighborhood, according to police.
Johnson told reporters his "gut feeling" was that the shooter in the killing of two-year-old Lavontay will also turn out to be a repeat gun offender. The toddler is believed to be 2 or 3 years old.
In a seperate incident, Kanari Gentry Bowers, 12, remains on life support after being shot 30 minutes before Holmes while paying basketball just a few miles away.
The death of the toddler marks the third time in the last several days that a child in Chicago has been a victim of the ongoing violence.
Ja'Mal Green, an activist in the city, said more gun laws and police will not reduce violence.
Chicago Mayor Rahm Emanuel has said he would welcome federal help and additional funding to complement the efforts of local law enforcement.