Ya think?
Now, therefore, be it known that I, Andrew Johnson, President of the United States, by virtue of the power and authority in me vested by the Constitution, and in the name of the sovereign people of the United States, do hereby proclaim and declare unconditionally, and without reservation, to all and to every person who directly or indirectly participated in the late insurrection or rebellion, a full pardon and amnesty for the offence of treason against the United States, or of adhering to their enemies during the late civil war, with restoration of all rights, privileges, and immunities under the Constitution and the laws which have been made in pursuance thereof.
Yeah, I think. Johnson issued two major amnesties while in office. The first, issued in 1865, didn't cover Davis. The one you quoted was issued on Christmas Day of 1868 and by that time Chief Justice Chase had made it clear that he believed that the 14th Amendment made prosecution of Davis impossible. Several weeks before the possibility of a Davis trial had died when Chief Justice Chase and Judge Underwood split on a vote to quash the indictment. Technically the indictment remained pending until dropped altogether the following February and Davis was a free man, pardoned for his crimes.