I don't know how true this is but I found this

"Dear Mrs. Davis... "It seems clear that General Lee was in fact pardoned by President Johnson, if not by the proclamation of July 4, 1868, then certainly by that of December 25, 1868, and that any politcal limitations to which he was subject by the Fourteenth Amendment were removed by the act of June 6, 1898....It is the opinion of the War Department that full and complete amnesty was accorded to General Lee by the several proclamations and acts of Congress above referred to, and that there remains no disability with respect to him upon which a further act of the Executive or of Congress could be operative even if he were still living."

Sincerely yours,

J.A. ULIO,

Major General,
The Adjutant General

James Alexander Ulio, Major-General (1882 – 1958)

http://www.gdg.org/Research/People/RELee/pardon.html

Amnesty is different than a pardon. Amnesty sets his status back to the day before he joined the Confederacy.

____________________
David Upton