The bottle contained trace amounts of heroin along with methadone, a prescribed drug used to treat heroin addicts, authorities said.
Police don't think the May 11 death was intentional, according to Tasha Jamerson, a spokeswoman with the Philadelphia District Attorney's Office.
Detectives believe father and son had fallen asleep after Orlando Rosado prepared the bottle for a 3 a.m. feeding. Rosado awoke to find the infant cold and limp in a pool of vomit.
Rosado, 45, waived a preliminary hearing Tuesday on third-degree murder, involuntary manslaughter, drug delivery causing death and other charges. He's being held on $1 million bail, which a judge refused to lower.
"We're actively investigating the case at this point," defense lawyer Bruce Wolf said, declining to elaborate.
Both Rosado and his girlfriend tried to resuscitate their child and called for help after finding him unresponsive.
Rosado had served at least a year in prison in a 2005 drug case, court records show.
In 2010, a Chester County man pleaded guilty to third-degree murder after admitting he had mixed methadone and the sleep-inducer Ambien into drinks for his 23-month-old son to keep him quiet. A prosecutor said the March 2009 death didn't appear intentional, though the drug levels found far exceeded the amount that would typically kill a child of that age. Ian Kohn, 31, of Phoenixville, is serving a 20- to 40-year prison term.