Calvin Edward Washington, 45, had served 14 years in prison for the rape and murder of a Waco woman. DNA testing last year found he did not rape the woman and testing earlier this year identified another man, Benny Carroll, as the rapist.
Carroll committed suicide in 1994 and samples of his DNA had been saved after the autopsy.
Additional testing on a bloody shirt found at Washington's home at the time of his arrest concluded that the blood did not come from the victim, the governor's office said.
The 16-member Texas Board of Pardons and Paroles unanimously recommended the pardon. The judge, prosecutor and sheriff involved in the case also supported the pardon.
Perry, who succeeded Gov. George W. Bush, has pardoned two inmates cleared through DNA testing. During the recent legislative session, he supported and signed legislation that allows for post-conviction DNA testing in certain cases.