In November, 1861, Augur was appointed Brigadier General of volunteers and assigned a brigade command in Brigadier General Irvin McDowell's Corps. In July, 1862, Augur was transferred to command a division under Major General Nathaniel Banks. Augur was severely wounded at the Battle of Cedar Mountain in August 1862. He was appointed Major General of volunteers by President Abraham Lincoln on November 14, 1862, with the date of August 9, 1862, as his effective date of rank. President Lincoln had to submit the nomination three times before the U.S. Senate finally confirmed the appointment on March 10, 1863.