Phoenix Police Chief Jeri Williams said today that investigators arrested Nathan Sutherland, 36, on one count of sexual assault and one count of vulnerable adult abuse.
Williams says Sutherland worked at the Hacienda HealthCare facility where the woman lived and had been providing care to her.
The 29-year-old victim - who gave birth to a boy at the centre on December 29 - has been in a "vegetative state" since the age of three.
The woman's parents said their daughter is not comatose but rather intellectually disabled because of seizures in early childhood.
While she doesn't speak, she has some mobility in her limbs, head and neck. She also responds to sound and can make facial gestures.
The family attorney said: "She has feelings, likes to be read to, enjoys soft music and is capable of responding to people she is familiar with, especially family."
Police said DNA testing of the nurse and the baby born to the woman led them to charge Sutherland with sexual assault.
Phoenix police spokesman Tommy Thompson said today that investigators obtained a court order to collect DNA from the licensed practical nurse.
Hacienda HealthCare employees said they had no idea she was pregnant.
Court records say her last known physical examination was last April.
A baby boy born to the woman will be cared for by the mother’s “loving family” after they revealed their “outrage” at the hospital rape.
Family Attorney John Michaels confirmed the child had been retained by the woman’s family, and said the infant boy would be "well cared for".
Meanwhile Phoenix police said during a press conference earlier this month that the Native American woman nearly died during birth when she went into labour.
Sgt Thompson said staff members of the facility were present at the baby's birth, and it was a natural delivery.
When asked if employees knew about the pregnancy and failed to report, Sgt Thompson said: “I'm led to believe that this [pregnancy] came to light when the baby was born.”
Police in Phoenix, Arizona, opened a criminal inquiry after it emerged the patient, who could not have consented to sex, had gone into labour at her private care home.
Soon after the news broke company boss Bill Timmons quit over the scandal as patients' family members questioned safety at the Hacienda chain of homes.
Terry Rambler, chairman of the San Carlos Apache Tribe based on a reservation east of Phoenix, said he was "deeply shocked and horrified at the treatment of one of our members".
Care workers at the Hacienda nursing home only realised the woman was pregnant when she began "moaning" and went into labour, according to reports.