Lee was defeated by the Army of the Potomac, commanded by General George Meade. But the Union General-in-Chief, U.S. Grant, was travelling with them in a mobile HQ, and it was Grant who took the surrender. Some said it should have been Meade.
General Joshua Chamberlain commanded the 1st Division of 5th Corp of the Army of Potomac which gave the Honour of The Arms formally accepting the surrender of the Confederate Army of Northern Virginia, on Apr.12, 1865.
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General Ulysses S. Grant was in command of the Union troops that formally accepted the surrender of the Confederate army. General Robert E. Lee surrendered to General Grant on April 9, 1865, effectively ending the American Civil War.
In August of 1945, the British Allies accepted the surrender of Japanese troops in southern Vietnam. Lord Mountbatten, who was the Supreme Allied Commander of the Southeast Asia Command accepted the surrender, and later the French reasserted control of Saigon.
The CSA Indians under Brigader General Stand Waite was a major force and he was the last Confederate General to surrender his command.
Confederate generals always had troops and slaves under their command.
Confederate General Longstreet
The Confederate General in overall command of the 1st Battle of Mannassas/Bull Run was Joseph E. Johnston but he left tactical command to P.G.T. Beauregard and officially shared command of the force present. The Confederate General in command of the 2nd Battle of Manassas.Bull Run was Robert E. Lee.