Barbour left office in January.
The pardons of 214 convicts, including four murderers, were challenged by state Attorney General Jim Hood, who said no required notice of the pardons was posted in newspapers, CNN reported.
The court majority said in its 77-page ruling the pardons "may not be set aside or voided by the judicial branch," and the decision on pardons rested "solely with the governor."
But Justice Michael Randolph dissented, saying the ruling was "a stunning victory for some lawless convicted felons, and an immeasurable loss for the law-abiding citizens of our state," CNN reported.
The four convicted killers receiving pardons were "trusties" who worked at the governor's mansion while Barbour was in office. CNN said all four have been monitored while the challenge worked its way through the courts.
Barbour's critics said he failed to consider the families of their victims before freeing the four.
Tiffany Brewer, whose sister Tammy was shot and killed by her husband David Gatlin as she held their 6-week-old baby, said the state high court decision was unfair.
Gatlin was among the pardoned trusties.
"Obviously all the laws in the Constitution don't have to be followed," a tearful Brewer told CNN.