The 29-year-old victim — who police said "was not in a position to give consent" — gave birth late last month to a baby boy, sparking an investigation.
The suspect's DNA was matched to that of the baby, leading to the arrest, according to police.
The suspect — identified as Nathan Sutherland, age 36 — faces charges of one count of sexual assault and one count of vulnerable adult abuse, Phoenix police Sergeant Tommy Thompson told a news conference.
Sutherland is a "licensed practical nurse who was responsible for providing care to the victim during this time the sexual assault occurred," Phoenix Police Chief Jeri Williams said.
Sex abuse probe launched after Arizona woman gives birth in coma
The police chief said she had not encountered a similar case during "30 years in law enforcement."
"The baby, I am told, is doing good," said Thompson.
"We can't always choose how we come into this life, but what we can choose to do as a community is love this child, and that's what we have the opportunity to do," he said.
A lawyer for the woman's family has said the infant "has been born into a loving family and will be well cared for," according to The New York Times.
The CEO of the nursing facility resigned following the scandal, according to a statement sent to media.
"This is a facility that you should be safe in and someone wasn't," Phoenix Mayor Thelda Williams said.
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