The child's grandparents were also home at the time of the baby's death but have not been charged.
Bond was set at $5 million. Thomas allegedly suffocated his son, Christopher Thomas, according to a Will County State's Attorney's office release.
Thomas is alleged to have pushed down on the child's head with his hand, suffocating the baby, according to the state's attorney's office. An autopsy found that Christopher died of suffocation, according to the Will County Coroner's office.
The STNG Wire contributed to this report.