Mary O'Callaghan, 48, was charged a day earlier in a felony assault case, according to the Los Angeles County District Attorney's Office.
The prosecutor's office said it will request $35,000 bail for the officer who, if convicted, could spend three years in state prison.
Tyler Izen, president of the Los Angeles police union,in a statement said "the alleged actions of the officer are incongruous with her reputation as an officer who was known to be diligent, courteous and ethical." O'Callaghan's lawyer Robert Rico describes his client, an 18-year veteran of the department, as "devastated."
"As an officer, a Marine and a mother, she's used to fighting and defending others," Rico said. "And she will fight and defend herself in a court of law to prove her innocence."
The charge stems from an incident July 22, 2012, when police investigating a possible child abandonment went to Thomas' home.
This was after Thomas had dropped off her two children at a police station because she felt her drug abuse had made her an unfit parent, according to Los Angeles County Supervisor Mark Ridley-Thomas.
At the mother's home, police talked with Thomas and arrested her.
It was then that O'Callaghan arrived on the scene, helping her fellow officers put Thomas -- then wearing handcuffs and leg restraints -- in a patrol car.
Video captured what happened next, the prosecutor's office said, including "O'Callaghan kicking Thomas in the stomach and groin area and pushing her in the throat."
Thomas lost consciousness in the patrol car, then was transported by paramedics to a hospital, where she was pronounced dead.
Prosecutors said they didn't file involuntary manslaughter charges against O'Callaghan because it couldn't be proven that she directly caused Thomas' death.
Her official cause of death was "undetermined," according to a coroner's report.
Thomas's relatives, though, believe O'Callaghan is responsible, family spokesman Najee Ali said Thursday.
The family is grateful for the charge filed this week, added Ali. But they're not satisfied yet, pushing for the public release of the video showing Thomas' final moments.
"We want to have the whole truth of what happened to Alesia Thomas," Ali said. "... This is not over with."