Police say 21-year-old Jason Quinones, of East 100th Street, is charged with rape and burglary.
The victim reportedly told police he attacked her while she slept.
She says she woke up to find him in her ground-floor apartment just after 5 a.m. Saturday.
He apparently entered through an open window and window gate.
Police say she woke up while being raped, and then chased the suspect into the hallway and out the front door.
The brazen attack had neighbors very concerned about the woman who was attacked.
"The person had to be very bold and desperate," neighbor Jackie Jenkins said.
"It just makes you more aware, you've got to be more aware of what's happening on the street," neighbor Debs Fewel said.
The victim was treated at the hospital.