A former nurse at the facility was arrested January 22 and charged with sexual assault.
The company announced the closure in a statement on February 7.
The crime came to light in December when the unidentified patient, a woman in her 20s, went into labor.
A frantic 911 call captured the scene, with a nurse at one point yelling, "The baby's turning blue!"
In a statement, Hacienda HealthCare said its board of directors "has come to understand that it is simply not sustainable to continue to operate our Intermediate Care Facility for the Intellectually Disabled", NBC News/Associated Press reported.
Hacienda HealthCare has been the focus of global attention after a baby was born to an incapacitated woman at one of their facilities.
"Immediately following the February 1 vote, we notified the State of Arizona of the Board's decision".
State agencies had issued an ultimatum after Hacienda HealthCare announced its decision to shut down Thursday.
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The alleged victim, who CNN is not naming because police are investigating the case as a sexual assault, had been at the long-term-care facility since 1992. "Hacienda intends to do everything possible to restore its credibility in the eyes of our patients, families, the community and our agency partners at every level", Hacienda said in a statement.
Investigators say Sutherland's DNA matched a sample from the woman's newborn boy, who is being cared for by her family. He has since given up his nursing license.
The news of the closure comes less than a month after nurse Nathan Sutherland was arrested and charged with sexual assault and vulnerable adult abuse.
The group that operates an Arizona health care facility where a severely disabled woman was impregnated past year will keep the unit open after reaching a deal with state officials, Hacienda HealthCare said Friday.
Arizona's governor Doug Ducey, who recently requested an investigation into how Hacienda employees did not notice that the unnamed patient had been raped, said the decision to move patients is 'very concerning'.
It would take weeks or months to transition all of them to other places.
Arizona state senators from left; Victoria Steele, Tyler Pace, Tony Navarette, Kate Brophy-McGee, Heather Carter, Rick Gray, Sylvia Allen, and Rebecca Rios meet in committee to discuss health care oversight at the Capitol in Phoenix, on Feb 6, 2019.
Arizona regulators have ordered Hacienda to contract with a third-party management company to assume day-to-day operations of the facility. "We want to find a path forward that is in the best interests of the patients - and this approach is not it". They also argued Hacienda contractually requires written consent from the state Department of Economic Security to close any operation. "State agencies are exhausting all efforts to bring this to a conclusion that is beneficial to the patients, some of whom have been at this facility almost their entire lives", the department said.