After the commutation, their prison sentences were set to end March 20.
Ramos was released on furlough to travel from prison in Phoenix, Arizona, to his home in El Paso, Texas, where he will serve the remaining portion of his sentence under house arrest, said his attorney, David L. Botsford of Austin, Texas.
After March 20, Ramos will be on "supervised release" -- similar to probation -- for up to three years, Botsford said.
Compean had been incarcerated in Elkton, Ohio, said U.S. Rep. Dana Rohrabacher, R-California.
"At last, Ramos and Compean have been rightfully reunited with their families," Rohrabacher said in a statement. "This day is long overdue. I wish the Ramos and Compean families the best as they now try to pick up the pieces and begin to heal from this terrible ordeal."
Both men had requested presidential clemency, and the U.S. Justice Department's Office of the Pardon Attorney was reviewing their requests when Bush made his decision, office spokeswoman Laura Sweeney said.
"The president has reviewed the circumstances of this case as a whole and the conditions of confinement and believes the sentences they received are too harsh and that they, and their families, have suffered enough for their crimes," a senior administration official said.
The official noted that both Democratic and Republican members of Congress had supported a commutation, including President Barack Obama's chief of staff, Rahm Emanuel, and Texas GOP Sens. Kay Bailey Hutchison and John Cornyn.
Department of Homeland Security Inspector General Richard L. Skinner, in a statement posted on the agency's Web site, confirmed that his staff wrongly told members of Congress last September that Compean had stated he "wanted to shoot a Mexican."