Surprisingly, Beauregard was wrong. The Confederate attack had achieved almost complete surprise. One Colonel reported to Sherman that there were troops in his front. Sherman however disregarded the report, "Beauregard is not such a fool as to leave his base of operations and attack us in ours. There is no enemy nearer than Corinth." However, now, this morning, Sherman's lines were being over run. With rebel yells, the Southerners achieved complete surprise, throwing back the Federals. However, the Northerners were veterans. The men of Sherman, Prentiss and McClernand formed along a ridge and opened a destructive fire on the advancing rebels. Beauregard established his headquarters at the Shiloh church, the Hebrew name for peace. From here Beauregard managed the battle from the rear, while Johnston rode along the front lines, encouraging the men. The Confederate assault soon stalled. The men scattered through the Federal camps, eating the hot breakfasts that the Federals were in the act of eating when they were driven off. The confusion of battle had displaced the corps lines which looked neat on paper.
On the far right of the Confederate line they encountered strong Union resistance around a 10 acre peace orchard. A heavy line of blue infantry beat back several Confederate brigades. Johnston arrived on the scene, and seeing the situation, said, "Men! they are stubborn; we must use the bayonet. I will lead you!" Standing up in his stirrups he led another attack forward against the line. Rushing behind him, the Confederate troops crushed through the Union defenses.
Riding out of the newly captured orchard, Johnston was elated at his victory. His coat was cut with bullets and a boot sole was cut in half, but he appeared unharmed. However, suddenly he began reeling in his saddle. The only staff officer with him was Governor Isham Harris of Tennessee, who had volunteered as an aide during for the battle. The governor asked if the general was hurt, and Johnston replied, "Yes, and I fear seriously." Laying him down on the ground, Harris soon found his wound. An bullet had cut an artery in his leg, and his boot was filled with blood. Harris did not know how to make a tourniquet, so he had to find a doctor. However, before the doctor could arrive, Johnston had bled to death. He died around 2:30 pm.
The fighting continued all along the Confederate line. In the center it was focused on a position called the Hornet's Nest, an open field bordered by a fence and a Sunken Road. From that road the Federals beat back wave after wave of gray attackers. However, with the capture of the Peach Orchard, there was a lull in the fighting as the Confederate shuffled their forces. The were able to get around the flank of the soldiers in the road, and 62 cannon were brought up to pour canister into the Yankee lines. When these guns opened, the Federal troops bent back in the face of the hard pressure. Wallace and Hurlbut's divisions broke towards the rear, only Prentiss's men remain firm. Surrounded on all sides, Prentiss continued to hold out. Finally at 5:30, after two hours of fierce fighting, Prentiss realized that further fighting was useless and surrendered his men, half of whom had been lost in the fighting. Although he had lost his command, Prentiss may have saved Grant.
Beauregard and his army had done well today. Although they had lost their commander and many other brave soldiers, they had surprised Grant and driven his lines back, capturing dozens of cannon and his entire division. Beauregard decided to delay the attacks until the next morning. However, not everyone agreed with him. There was the danger that Buell's army might arrive during the night, giving Grant fresh troops to use the next day. Nathan Bedford Forrest had seen Buell's men arriving during the next at Pittsburg Landing. While the soldiers were trying to sleep in the falling rain, Forrest searched for Beauregard, urging every general he could find to launch a night attack before the new troops could be positioned. However, he never found Beauregard no one else would do it, so he gave up, convinced that the Confederates would be whipped the next morning.