Jones, 30, had been prescribed methadone to wean her off her addiction to painkillers.
The powerful opioid, which comes in a syrup form, is often given to addicts but it is extremely dangerous if it enters a child's body.
Jones, who appeared in court in the suburbs of Philadelphia on Friday, July 13, admitted she had been taking methadone during her pregnancy and since the baby, known as R.J., was born.
Autopsy Shows Drugs Cocktail
An autopsy found R.J. died after going into cardiac arrest having become intoxicated with "a combination of methadone, amphetamine and methamphetamine" through the breast milk.
Bucks County District Attorney's Office said the child was found pale and with bloody mucus coming from his nose at 7am on April 2 in a house in Chalfont, north of downtown Philadelphia.
When interviewed by police Jones said she had breastfed R.J. at 3am "because she was too tired to go downstairs and make a bottle of formula."
Grandmother Tried In Vain With CPR
Jones called her mother, who called 911 and then tried in vain to save the child with CPR.
Paramedics rushed R.J. to hospital, where he was declared dead.
Jones admitted she often breastfed the baby but her attorney, Louis Busico, said she never intended him any harm.
"Samantha Jones has suffered the biggest loss any human being can suffer — the loss of a child," Ms. Busico told the Bucks County Courier Times.
Jones remains in custody until July 23, as the judge has set bail at US$3million and her family are not wealthy.
Pennsylvania is one of many states in the Appalachian region of the United States which has suffered from high rates of opioid addiction, including methamphetamines, codeine, morphine, Xanax and Vicodin.