[2] Following his graduation, Augur served as aide-de-camp to Generals Hopping and Cushing during the Mexican–American War, and during the 1850s took an active part in the campaigns of the western frontier against the Yakima and Rogue River tribes of Washington and, in 1856, against the Oregon Indians.

[4] The American Civil War was just over four months old when Augur was made Commandant of Cadets at West Point on August 26, 1861, replacing John F. Reynolds who, newly promoted to Brigadier General, had left that position on June 25, 1861, to perform other military duties.

Major General Augur was in command at Baton Rouge, Louisiana, on May 2, 1863, where he unexpectedly received Colonel Benjamin H. Grierson leading his tattered and exhausted volunteer Brigade of Union cavalrymen from their sixteen-day, 600 mile raid (Grierson's Raid) behind Confederate lines in Tennessee, Mississippi and Louisiana.

[9] During the Siege of Port Hudson, which lasted from April 27 to July 9, 1863, Augur commanded the First Division in the XIX Corps of Major General Bank's Army of the Gulf.

[4] After the fall of Port Hudson, Augur was assigned command of the XXII Corps and the Department of Washington which he held from October 13, 1863, to August 13, 1866.

[4][13][11] Augur was one of the Army officers who were present at the Petersen House where the mortally wounded President Abraham Lincoln was taken after he was shot by John Wilkes Booth.

[16] Throughout that fateful night, and in the following days, Augur was instrumental in mobilizing troops in his command to pursue and eventually capture Booth and his co-conspirators,[17] including detailing the detachment of the 16th Regiment New York Volunteer Cavalry under the command of Lt. Edward P. Doherty[18] to follow a lead given to Stanton by a Union spy which eventually led to Lt. Doherty and his detachment tracking down and cornering President Lincoln's assassin, Booth, and his associate, David Herold, in a tobacco barn near Port Royal, Virginia.

[20] On Wednesday, April 19, 1865, Augur served as the officer in charge of the military procession that escorted the president's body from the White House to the Capitol where it lie in state.