If the Supreme Court would have refused to issue a stay, the previous stay was set to expire at 8 a.m. Monday.
"I believe the Court made the correct decision to issue a stay," Utah Gov. Gary Herbert said in a statement Friday afternoon. "...Regardless of where you stand on same-sex marriage, all Utahns deserve clarity and finality when it comes to the law."
But in the decision to stay, Utah American Civil Liberties Union legal director John Mejia said those same-sex couples married last December are missing out on important spousal benefits.
Had the stay not been issued, Mejia said some of the couples could have finalized their proof of adoption. They could have added their spouse to their health insurance. They could have applied for insurance discounts.
But for now, they'll continue to wait. Mejia said they are hoping to get their case expedited and heard in front of the 10th Circuit of Appeals as soon as possible.
" The quicker we can work through this recognition, the better," Mejia said.
Megan Berrett and Candice Green-Berrett were married Dec. 20. Green-Berrett is their daughter's biological mother. In anticipation of Monday, the couple met with lawyers to ensure their papers were in order so Berrett could adopt their daughter. They did not think the Supreme Court would grant the emergency stay.
"We're very frustrated, because I think we got our hopes up, and now the idea that I'm going to have to wait a year to adopt Quinn is frustrating to say the least," Berrett said. "This is our family hanging in the balance. This is my 10-month-old daughter's life that we're playing with, and staying our marriage doesn't do anything but hurt kids."
Though Mejia said he felt disappointed with the stay, he believed the Supreme Court's Friday decision was "not at all a comment on the merits" of their case.
Utah asked for the emergency order on Wednesday, saying that the state believes it will ultimately prevail in its fight to revive a ban on same-sex unions. If it loses, the state said it would work to nullify the marriages entered into during that window.
However, the ACLU argued to the Supreme Court that the state should not be allowed to "effectively divorce" them by placing their unions on hold. The ACLU also said that even if the same-sex marriage ban is revived, the state will be constitutionally barred from nullifying the marriages that took place between Dec. 20, 2013, and Jan. 6, 2014. It said that "couples that do legally marry are protected by the same fundamental rights and liberty interests as any other legally married couple."
Utah continues to defend its right to define marriage as a union between one man and one woman on two fronts in Evans. v. Utah and in the Kitchen v. Herbert case that in December toppled the state's ban on same-sex unions.
Kimball ruled in May in the Evans case that Utah must recognize and imbue all same-sex marriages performed in the state with the same rights and privileges afforded to married opposite-sex couples. His decision did not go into effect immediately to give the state time to appeal.
Utah's emergency application was filed with U.S. Supreme Court Justice Sonia Sotomayor, who oversees the federal court circuit of which Utah is a part and who, in January, halted the issuance of marriage licenses to same-sex couples in Utah after 17 days of marriages.
Harry Stevens contributed to this report.