Jannie M. Perry, 38, is charged with first-degree murder, concealment of a homicidal death, and obstructing justice.
Damari's brother, Jeremiah Perry, has also been charged in his death.
Additionally, a minor sibling was arrested and is in juvenile jail.
Damari was reported missing on Jan. 5 by Jannie in North Chicago.
He was found dead last Friday night in an abandoned alley in the 700 block of Van Buren Street in Gary, Indiana.
At first, Jannie said he was last seen in Skokie with his 16-year-old sister at her friend's home on Tuesday, Jan. 4 around 3 p.m.
The initial story provided to police by the family stated that Damari and his sister were driven to a party in Skokie by a Black woman, who was only known as "Monique," and a Black man, who was known as "Wacko" or "Chaos."
Jannie said she had no idea where the friend's house was located in Skokie.
Damari's sister allegedly described the apartment building where the party took place as possibly being a 3-story yellow building with an exposed stairway.
Jannie said her daughter was drinking, fell asleep and when she woke up her little brother was gone, and so was "Wacko."
Jannie Perry, 38
The sister then said she was driven back to her North Chicago home by Monique, without her brother.
Damari was reported missing Wednesday, Jan. 5, just before 5 p.m. when the sister allegedly got home.
After further investigation into Damari's disappearance, police determined that the story provided by the family was false.
Prosecutors believe Damari was "punished" and killed on Dec. 29 because he did something to Jannie to which she believed he should be punished.
Damari was allegedly put in cold water in a bathtub or shower in their home in North Chicago, and eventually started vomiting and passed out.
He was taken out of the cold water; no one called 911, and he died.
Prosecutors believe Jeremiah and Jannie talked about disposing the body, and decided to dump him in Gary.
According to the Lake County Coroner's Office, Damari was found naked and wrapped in a plastic trash bag and partially charred in the alley in Gary.
Dr. Zhou Wang of the coroner's office "found scattered ecchymosis on the right leg, extremely cold core temperature, and partially frozen internal organs."
Additionally, Dr. Wang said there was "postmortem thermal injury/charring over the body."
Based on the findings, the coroner's office said the pending cause of death is Hypothermia. The manner of death was determined to be homicide.
Police said Jannie was taken to the hospital Saturday after complaining that she was ill.
She was then able to appear in bond court Wednesday where a judge set bond at $5 million.
Her next scheduled court date is Feb. 8.