With the coming of the Civil War, CPT Garnett resigned his US commission on 17 May 1861. He was commissioned Major CSA, and in November 1861 Brigadier General in the Provisional Army. Subsequently, he was appointed second-in-command of then Colonel Thomas R.R. Cobb's Georgia Legion, and promoted to Lieutenant Colonel in early September. After brief service with the legion on the Peninsula, Garnett received his promotion to Brigadier General and was immediately assigned to the Shenandoah Valley, coming under command of General Thomas J. Jackson. By spring 1862, BG Garnett commanded Jackson’s old troops, now known as the Stonewall Brigade. He commanded the Stonewall Brigade in the Shenandoah Valley campaign and at Kernstown, 23 Mar 1862. During the Maryland campaign he commanded Pickett's brigade. General Garnett commanded a brigade in Pickett's Division consisting of the Eighth, Eighteenth, Nineteenth, Twenty-eighth and Fifty-sixth Virginia regiments, which he finally led in "Pickett's Charge" on the third day of the battle of Gettysburg. The brigade went into action with 1,287 men and 140 officers, and after the fight only about 300 effectives remained. General Garnett's part in this fatal action is thus reported by his successor in command, Maj. Charles S. Peyton:
"Of our cool, gallant, noble brigade commander it may not be out of place to speak. Never had the brigade been better handled, and never has it done better service in the field of battle. There was scarcely an officer or man in the command whose attention was not attracted by the cool and handsome bearing of General Garnett, who, totally devoid of excitement or rashness, rode immediately in rear of his advancing line, endeavoring, by his personal efforts and by the aid of his staff, to keep his line well closed and dressed. He was shot from his horse while near the center of the brigade, within about 25 paces of the stone wall." Source: Confederate Military History, vol. IV, p. 597
BG Garnett's burial location is unknown. It is believed that his body was stripped of valuables and buried in a mass grave of CSA soldiers at Gettysburg. It may have been later recovered and reinterred in Hollywood Cemetery in Richmond, Virginia. His sword was discovered in a Baltimore pawn shop some years later and returned to the family.
His cousin, BG Robert Seldon Garnett, was killed commanding CSA forces at the battle of Corrick's Ford on 13 Jul 1861. Son, William P. Garnett, served the U.S. Army as an interpreter and "scout" working primarily from the Pine Ridge Reservation. BG Garnett is survived by numerous living descendants of his son.
One last note. There is some controversy about the various photographs said to be of BG Garnett with some scholars convinced that all those identified as Richard are of his cousin Robert.