Jose Hilario Abreu, 28, is charged with involuntary manslaughter, prosecutors said in a release Friday.
Borgen was shot on the 900 block of East Hamilton Street on March 28 and rushed to Lehigh Valley Hospital-Cedar Crest where he succumbed to his injuries, city police said previously.
On Friday, the DA's Office said Abreu had placed a loaded handgun under a sofa where Borgen and a 2-year-old were sitting, then left the room.
While in the other room, Abreu told police he "heard a loud bang and returned to find Elijah suffering from a gunshot wound to the chest."
"Evidence further revealed that when the gun was discharged, it was unholstered and resting atop a pillow on the couch where both toddlers were sitting," prosecutors said.
A rapid gunshot residue test after Borgen's death showed "a presumptive positive indication for gunshot residue on his hands," they added.
In addition to the involuntary manslaughter count, Abreu is charged with two counts of endangering the welfare of children, they added.
According to court records, Abreu was unable to post $250,000 bail at his arraignment on Friday. His preliminary hearing before Magisterial District Judge Ronald S. Manescu is scheduled for Friday, April 12.
Loved ones are collecting donations for Borgen's memorial on GoFundMe.
Click here to follow Daily Voice Chambersburg and receive free news updates.