The higher court had blocked the release after Superior Court Judge Ripley Rand ruled that the two inmates, who are serving life sentences, should go free.
Judge Rand said that the Department of Correction is wrongly interpreting its regulations on sentence-reduction credits.
Jones and Brown are two of several dozen inmates sentenced to life in prison in the 1970s, but the courts have ruled that the law at that time meant a life sentence was 80 years, and the inmates say with time off for good behavior, they should be released.
Other inmates have also asked to be released, but judges have not yet ruled on their cases.
Governor Beverly Perdue has been very vocal about her opposition to free the inmates. Monday she told reporters at Camp Lejeune she is "furious with Judge Rand's decision."
"I've been in politics a long time, and I've never been as disgusted with the system in my life," Perdue said.
The state now has until 5 p.m. Friday to respond. A spokesman said an appeal would be filed with the North Carolina Supreme Court.