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Timeline
1872 - Detail
May 22, 1872 - Civil rights are restored to citizens of the South, except for five hundred Confederate leaders, with the passage of the Amnesty Act of 1872 and its signing by President Ulysses S. Grant.

The Civil War may have ended in 1865 symbolically at Appomattox Court House, but the work of repair, passage of the Civil Rights Acts for black citizens, and Reconstruction took first precedence to the Congress and President in the years soon after, albeit, pardons and amnesty were not far behind.
There had been, of course, some amnesty and pardon activity during the seven years in between. President Abraham Lincoln had even issued several proclamations on the subject prior to the end of the Civil War. President Andrew Johnson offered pardons to several groups of Confederate citizens. In 1868, Johnson granted unconditional amnesty to most remaining participants of the rebellion, those below the rank of colonel. There were caveats to most of those pardons and amnesties, particularly to the higher politicians and generals in the Confederacy.
On May 22, 1872, Congress finally passed the General Amnesty Act, immediately signed into law by President Grant, considering it another reconstruction measure to bring both halves of the nation together. It removed some of the restrictions in Section Three of the 14th Amendment, such as political disabilities, such as the right to vote from the general public or hold office, except for certain people. Thaddeus Stevens, in the House of Representatives agreed with the harsher measures in the above, even to the point of disallowing any vote by supporters of the Confederacy until 1870, but in the end, most in the Senate disagreed with going quite that far, and Section Three read like this ...
"No Person shall be a Senator or Representative in Congress, or elector of President and Vice President, or hold any office, civil or military, under the United States, or under any State, who having previously taken an oath, as a member of Congress, or as an officer of the United States, or as a member of any State legislature, or as an executive or judicial officer of any State, to support the Constitution of the United States, shall have engaged in insurrection or rebellion against the same, or given aid or comfort to the enemies thereof. But Congress may by a vote of two-thirds in each House, remove such disability."
As states were allowed to rejoin the Union, starting in 1870 with Texas, Mississippi, and Virginia, tensions rose as to how or who would qualify to be members of the House of Representatives or Senate from those states. To ease those tensions, President Grant proposed the General Amnesty Act of 1872, some calling it the Confederate General Amnesty Act, allowing all but five hundred individuals the right to seek office, including "Senators and Representatives of the 36th and 37th Congresses, officers in the judicial, military, and naval service of the United States, heads of departments, and foreign ministers of the United States." One hundred and fifty thousand former Confederates, however, were now allowed to hold office.
Full Text, Amnesty Act 1872
May 22, 1872
CHAP. CXCIII - An Act to remove political Disabilities imposed by the fourteenth ArticleArticle of the Amendments of the Constitution of the United States.
Be it enacted by the Senate and House of Representatives of the United States of America in Congress assembled (two-thirds of each house concurring therein), That all political disabilities imposed by the third section of the fourteenth article of amendments of the Constitution of the United States are hereby removed from all persons whomsoever, except Senators and Representatives of the thirty-sixth and thirty-seventh Congresses, officers of the judicial, military, and naval service of the United States, heads of departments, and foreign ministers of the United States.
APPROVED, May 22, 1872
President Grant followed up the act with a Proclamation on June 1, 1872, that told district attorneys to halt prosecutions of those pardoned by the act, except those that fell into the exceptions. It included a Presidental Pardon of all but five hundred Confederate leaders.
What happened to the more famous Confederate leaders and were they part of the five hundred who were not pardoned by Grant? U.S. Grant had paroled Robert E. Lee at Appomattox and allowed him to reunite with his wife. Confederate President Jefferson Davis was captured and held in prison at Fort Monroe. He was released on $100,000 bail in 1867, paid in part by some of the same Northern abolitionists who had bankrolled John Brown's attack at Harpers Ferry in 1859. Davis came to trial for treason on December 3, 1868; that trial ended in a 1-1 tie, and thus was pushed up to the Supreme Court. On December 25, 1868, President Andrew Johnson agreed to pardon the rest of the Confederate Army, ... that included Davis. On February 15, 1869, the Federal Government dropped all charges.
But you didn't anwer your initial question? That's correct. We have not yet been able to find that list of five hundred, but it is assumed that both Robert E. Lee and Jefferson Davis were part of it.
Photo above: Montage (left) Portion of engraving of President Andrew Johnson pardoning Rebels at the White House, 1865, Stanley Fox, Harpers Weekly; (center) portin of engraving of Thaddeus Stevens calling for Johnson's impeachment, 1868, Theodore R. Davis, Harpers Weekly; (right) President U.S. Grant, 1865/1880, Brady-Handy Collection. All courtesy Library of Congress. Below: Engraving of Jefferson Davis in prison at Fort Monroe in 1866, 1866, John J. Craven. Courtesy Wikipedia Commons. Info Source: National Archives; "The General Amnesty Act of 1872: A Note," James A. Rawley; "Amnesty and Section Three of the Fourteenth Amendment, Gerard N. Magliocca; "The Amnesty Act of 1872," potusgeeks.livejournal.com; legisworks; constitutioncenter.org; "Post-war treatment of High Ranking Confederate Leaders," Clint Johnson, Essential Civil War Curriculum; Wikipedia Commons.
