Juvenile Court Judge Scott Johansen rescinded his order, according to court documents obtained by CNN on Friday.
He amended Tuesday's first ruling, crossing out the line in the order that read, "The Court orders the Division to place the child with a duly married, heterosexual foster-adoptive couple within one week."
Court documents show Johansen wrote initially that it was not in the best interest of children to be raised by same sex couples, citing "belief that research has shown that children are more emotionally and mentally stable when raised by a mother and father in the same home ..."
Johansen, in his amended order, struck the sentence about the best interest of children and scratched out "belief" and replaced it with "concern."
"The judge is clearly reacting to adverse publicity and critical comments regarding his controversial previous ruling," said CNN legal analyst Paul Callan after reviewing the court documents.
Callan said the change suggests that the judge was worried about his order "being viewed as an application of religious belief rather than an application of the law."
The court documents show there will be future hearings related to the case. The baby will stay with the couple in the interim.
The original decision left the parents, April Hoagland and Beckie Peirce heartbroken and shattered.
"It's not fair, and it's not right, and it hurts me very badly, because I have done nothing wrong," Hoagland told CNN affiliate KUTV.
The couple was legally married more than a year ago and approved as foster parents after passing home inspections, background checks and interviews with the division of family services. They want to adopt the infant.
They already are raising Peirce's two children. They say the Utah Division of Child and Family Services, the biological mother and others involved in the case are supportive of them.
The child services division subsequently filed a motion asking the judge to stay his order. If he did not, the agency had said that it would petition a court of appeals.
The case sparked outrage and cries of injustice from rights groups and others.
The Human Rights Campaign, the nation's most prominent LGBT civil rights organization, is calling for an investigation into Johansen.
"Removing this child from a loving and permanent home based solely on the sexual orientation of its parents is not only discriminatory, but is also counter to the overwhelming evidence that children being raised by same-sex parents are just as healthy and well-adjusted as those with different-sex parents," said HRC Legal Director Sarah Warbelow in a statement Friday.
"It is unconscionable that any judge would let bias interfere with determining the true best interest of a child and we strongly encourage the commission to take appropriate action to hold this judge accountable and to affirm that personal bias has no place in judicial decisions in Utah."
Even the governor's office has weighed in.
"I expect the court and the judge to follow the law. He may not like the law, but he should follow the law," said Gov. Gary Herbert. "We don't want to have activism of the bench in any way, shape or form."
This was the first serious challenge on same-sex adoption rights since a U.S. Supreme Court ruling legalized same-sex marriage this summer, Callan said.
"This is the first time there has been an attempt to deprive gay foster parents of their rights to care for an adoptive child," said Callan.
He said he expects to see a second wave of cases related to same-sex marriages, such as adoption, employment and other issues that the Supreme Court did not address.
"We want to do what's best for the child and make sure she's taken care of in the way she should be," Peirce told Ashleigh Banfield of CNN's "Legal View" before the judge rescinded the ruling. "We don't want her bouncing back and forth."