Phoenix Police Chief Jeri Williams said 36-year-old Nathan Sutherland was arrested and will be charged with one count of sexual assault and one count of vulnerable adult abuse for the incident.
"We have worked virtually non-stop every day, every night to resolve this case," Chief Williams told reporters, adding that the crime was "beyond reproach".
The chief said that police used "good old-fashioned police work" in addition to DNA tests on the baby to find a match and made the arrest. Sutherland had worked at the facility since 2011, officials added.
"We owed this arrest for the victim, we owed this arrest of the newest member of our community, that innocent baby," Chief Williams said.
At the time of the incident, employees said they had no idea she was pregnant while court records show her last recorded medical check up was in April 2018.
Investigators say they may not ever know how many times the woman was sexually assaulted.
Police say Sutherland was responsible for the woman's care at the time on the assault.
The surprise birth late last month triggered reviews by state agencies and highlighted safety concerns for patients who are severely disabled or incapacitated. It also prompted authorities to test the DNA of all the men who worked at the Hacienda HealthCare facility.
Sutherland submitted his DNA sample under court order on Tuesday and the results came back a few hours later, showing he was a match to the baby. He declined to speak with police and invoked his Fifth Amendment rights, Thompson said. A message left at a phone number listed for Sutherland was not immediately returned.
Hacienda officials fired Sutherland yesterday after learning of his arrest. The company said it was "troubled beyond words." Sutherland had passed an extensive background check.
"Once again, we offer an apology and send our deepest sympathies to the client and her family, to the community and to our agency partners at every level," Hacienda said in a statement.
The 29-year-old victim has been in long-term care since the age of 3 and gave birth at the facility on December 29. As her guardian, the woman's mother was required to submit an annual report to the court that included results of a medical exam.
The case has prompted the departure or discipline of key figures at Hacienda HealthCare, including the CEO. The provider on Sunday announced that one doctor who had cared for the woman resigned and another had been suspended.
Earlier stories had described the patient as being comatose or in a vegetative state. But her parents released a statement on Tuesday disputing that characterisation. They described her instead as 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.