In October 1861, Thomas became colonel of the 35th Georgia Infantry. The regiment was attached to Brigadier General Joseph R. Anderson's brigade, which was initially stationed in Georgia but during the Peninsula Campaign was sent to the Richmond area to reinforce Joe Johnston's army. On May 27, 1862, the brigade was added to the newly created division of Major General A.P. Hill, soon to be known as the "Light Division". While commanding the regiment, Thomas suffered a minor wound at the Battle of Beaver Dam Creek (Mechanicsville) during the Seven Days Battles. Anderson was wounded at Glendale and afterwards resigned his commission to manage the Tredegar Iron Works in Richmond. Thomas then became permanent commander of the brigade, and on November 1 he was promoted to brigadier general, participating in all of the major battles and campaigns fought by the Army of Northern Virginia.
When division commander William D. Pender was mortally wounded at Gettysburg, the two ranking brigade commanders left in the division were Thomas and James H. Lane. Although both had been promoted to brigadier general the same day (November 1, 1862), Lane had received his colonel's commission in September 1861, a month before Thomas had become a colonel, and thus Lane outranked him and assumed temporary command of the division. It has been suggested that as a Georgian, Thomas was not favored in a division with two North Carolina brigades. He remained in command of his brigade until the Confederate surrender at Appomattox Court House in 1865.
Huff, Frederick Ware. Four Families: Winn, Thomas, Ware, Garrett of the Southern United States from 1600s to 1993. Kennesaw, GA: Frederick Ware Huff, 1993. OCLC29382913.
Sifakis, Stewart. Who Was Who in the Civil War. New York: Facts On File, 1988. ISBN978-0-8160-1055-4.
Warner, Ezra J.Generals in Gray: Lives of the Confederate Commanders. Baton Rouge: Louisiana State University Press, 1959. ISBN978-0-8071-0823-9.