Libby was convicted of lying to investigators probing the outing of CIA operative Valerie Plame. He was sentenced to 30 months in prison, two years probation and a $250,000 fine. Bush threw out the jail time but left the probation and fine intact.
Libby had sought to remain free on bail while appealing his conviction, but the 4th U.S. Circuit Court of Appeals Monday rejected his request, saying it was unlikely his conviction would be overturned.
Bush said in a statement that while he had said earlier it would be inappropriate to comment or intervene until Libby's appeals had been exhausted, he acted because Libby's incarceration was imminent.
"I respect the jury's verdict. But I have concluded that the prison sentence given to Mr. Libby is excessive," Bush said.
The former vice presidential aide was convicted of lying even though no one was charged with the actual leak to columnist Robert Novak.
Senate Majority Leader Harry Reid, D-Nev., called the president's actions "disgraceful," the Chicago Tribune reported.