Amy Sandler and Niki Quasney, who married in Massachusetts last year, asked for an emergency order because Quasney has been diagnosed with terminal ovarian cancer. U.S. District Judge Richard Young's ruling does not affect the ongoing legal fight over same-sex marriage in Indiana.
Young granted the couple a temporary order last month that expired Thursday. His new ruling extends that indefinitely.
The state attorney general's office issued a statement suggesting it will appeal.
"The motion should not have been granted since the current rule of law does not allow for a hardship exception from the statute for one person or two people, as that would create inconsistency for all other citizens of Indiana," officials said.
Gay rights activists are seeking an order, like the one recently issued in Ohio, that would require the state to recognize same-sex marriages performed in states where they are legal. Young has not yet ruled on a request to decide the issue without a trial.
The Ohio ruling has been stayed pending appeal.
"We are relieved and happy to send our congratulations and best wishes to Amy, Niki and their family," Lambda Legal, which is representing the couple, said in a statement. "We applaud their courage and commitment to each other and to equality as they fight Niki's illness."
Same-sex marriages are now legal in 17 states, the District of Columbia and some Native American tribal jurisdictions. In the first states, the change came about by court order but more recently a number of states have legalized gay marriage by referendum or legislative action.