Besides the physical exhaustion of the rebels on Sunday, other causes worked on their side to bring about their final failure. The most hurtful of these was no doubt the killing of their Commander-in-chief, General A. S. Johnston, between two and three P.M. on Sunday. While riding with the attacking columns, he was struck by several bullets, one of which cut an artery and made him bleed to death in fifteen minutes. His death was probably a greater blow to the Confederacy than the defeat of his purpose, for, according to the testimony of all who knew him personally, on the Southern as well as on the Northern side, there was the stuff for another Robert E. Lee in him, and he might have proved as formidable an antagonist on the western as the latter on the eastern theatre of war. Jefferson Davis fully recognized this in his official lament over the Confederacy's irreparable loss. Perhaps even the result at Shiloh would have been different if Johnston had lived. Leaving his admittedly inferior capacities as a strategist out of consideration, Beauregard was not in bodily condition for an energetic exercise of the chief command, being just convalescent from a severe two months illness.
Another cause appears from the admission of Beauregard in his report that “officers, non-commissioned officers and men abandoned their colors early in the first day to pillage the captured encampments,” and that “others retired shamefully from the field on both days, while the thunder of cannon and the roar and rattle of musketry told them that their brothers were being slaughtered by the fresh legions of the enemy.” The General claimed, on a later occasion, that the casualties on the first day and the admitted skulking of a portion of his command had reduced his fighting strength to twenty thousand on the second day, and this number may be accepted as correct. General Braxton Bragg complained as strongly of the straggling and plundering of his men, and ascribes to the weakness and confusion caused by it the failure to finish the battle on the first day.