The Legislature last month approved the legislation that does away with provisions of the act. The 2009 law allows death row inmates to use statistics in a new type of court hearing to argue racial bias played a role in their sentences.
Perdue said in a statement that she's a strong supporter of the death penalty.
"However, because the death penalty is the ultimate punishment, it is essential that it be carried out fairly and that the process not be infected with prejudice based on race," she said.
Many of the state's prosecutors have said the law is too broad and only factors in race - not the circumstances of a case. They also say if the act isn't repealed, it will clog up state courts.
There are currently 157 inmates on death row in North Carolina. The prosecutors say all but five have filed to have their cases reviewed under the Racial Justice Act. Fifty-two are cases where the defendant was white, the victim was white, and the jury was all white.
Opponents of repealing the law - like the NAACP - say it insures race doesn't play a part in sentencing people to death.
Perdue's decision means she must call the Legislature back to Raleigh by Jan. 8 to consider an override. Lawmakers may find that difficult to do, especially in the House, where it passed in June along party lines. Republicans are a few votes shy of a veto-proof majority in the chamber.
"I am disappointed in yet another decision by Gov. Perdue to put politics ahead of principle," House Speaker Thom Tillis, R-Mecklenburg, said in a prepared statement, adding the governor has turned her back on the families of victims across this state and a vast majority of prosecutors who need every available resource to crack down on violent criminals."
The governor's veto came two days after she met with relatives of murder victims and victims of violent crimes at the old Capitol building in Raleigh. Some of those relatives asked her to keep the act on the books.
"We applaud her for understanding that racially-biased justice is not justice at all and for reaffirming that she values the lives and the safety of all citizens regardless of race," according to a statement from Murder Victims' Families for Reconciliation, which asked Perdue for a veto.
North Carolina and Kentucky are the only states in the country with these types of laws.