Due to his previous field experience in the Corps of Engineers, Newton received the rank of brigadier general in September 1861. He served in the defense of Washington. During the Peninsula campaign, Newton was transferred to a field command in charge of a division of the VI Corps. He served in the Battle of Antietam, and at the Battle of Fredericksburg. In March 1863, following testimony to the Committee on the Conduct of the War, Nelson was promoted to major general. In the 2nd Battle of Fredericksburg, during the Chancellorsville campaign, he led his forces in the attack on Marye's Heights. During the battle of Gettysburg, Nelson was put in command of I Corps after the death of General John F. Reynolds. In the spring of 1864, his command was broken apart, and he was reassigned to the western theater. In the Atlanta campaign, Nelson served in command of a division in the IV Corps of the Army of the Cumberland. Later he was reassigned to the district of West Florida, until the end of the war. Nelson was brevetted a major general in 1865.
