Parker was present when Confederate general Robert E. Lee surrendered at Appomattox Courthouse in April 1865. He helped draft the surrender documents, which are in his handwriting. At the time of surrender, General Lee "stared at me for a moment," said Parker to more than one of his friends and relatives, "He extended his hand and said, 'I am glad to see one real American here.' I shook his hand and said, 'We are all Americans.' Parker was brevetted brigadier general of United States Volunteers on April 9, 1865, and of United States Army March 2, 1867.