Prosecutors say the bottle contained trace amounts of heroin along with methadone, a prescribed drug used to treat heroin addicts.
Officials don't think the May 11 death was intentional, according to spokeswoman Tasha Jamerson of the Philadelphia District Attorney's Office.
She says Orlando Rosado awoke to find the infant cold and limp in a pool of vomit. Police believe father and son had fallen asleep after Rosado prepared the bottle for a 3 a.m. feeding.
The 45-year-old Rosado waived a preliminary hearing Tuesday on third-degree murder and other charges. He's being held on $1 million bail.
Defense lawyer Bruce Wolf says he is actively investigating the case.