The pardon proclaims Earl Washington Jr.'s innocence in the June 1982 rape and murder of Rebecca Lynn Williams, a 19-year-old mother of three.
Washington, who is mildly retarded, falsely confessed and then recanted. Last year, a federal jury found that a now-deceased investigator fed him details of the crime to produce the confession.
In 2000, DNA testing implicated a convicted rapist, Kenneth Maurice Tinsley, who pleaded guilty in April to killing Williams.
Gov. Jim Gilmore had pardoned Washington in 2002, but that pardon did not mean he was innocent, only that a jury would not have convicted him in light of the DNA evidence.
"It is now evident that Mr. Washington was and is innocent of the crimes against Mrs. Williams," Kaine wrote in the pardon, issued Tuesday. "I have decided it is just and appropriate to grant this revised absolute pardon that reflects Mr. Washington's innocence."
Washington said in a telephone interview that official acknowledgment of his innocence was important to him.
"It makes me feel good that the governor did that," he said.
Washington, 47, who has married since his release and is a maintenance worker in Virginia Beach, settled his lawsuit against the state for $1.9 million.