Jackson learned at 7 a.m. that the Federals were approaching his column. Without proper reconnaissance or waiting for the bulk of his force to come up, he ordered Winder's Stonewall Brigade to charge through the thinning fog. The brigade was caught between artillery on its flank and rifle volleys to its front and fell back in disarray. They had run into two brigades at the vanguard of Shields's army, 3,000 men under Brig. Gen. Erastus B. Tyler. Attempting to extricate himself from a potential disaster, Jackson realized that the Union artillery fire was coming from a spur of the Blue Ridge. Jackson and Winder sent the 2nd and 4th Virginia Infantry regiments through the thick underbrush up the hill, where they encountered three Union infantry regiments supporting the artillery and were repulsed.

After his assault on the Coaling failed, Jackson ordered the rest of Ewell's division, primarily Trimble's brigade, to cross over the North River bridge and burn it behind them, keeping Frémont's men isolated to the north of the River. While he waited for these troops to arrive, Jackson reinforced his line with the 7th Louisiana Infantry of Taylor's brigade and ordered Taylor to make another attempt against the Union batteries. Winder perceived that the Federals were about to attack, so he ordered a preemptive charge, but in the face of point-blank volleys and running low on ammunition, the Stonewall Brigade was routed. At this point, Ewell arrived on the battlefield and ordered the 44th and 58th Virginia Infantry regiments to strike the left flank of the advancing Union battle line. Tyler's men fell back, but reorganized and drove Ewell's men into the forest south of the Coaling.

Taylor attacked the infantry and artillery on the Coaling three times before prevailing, but having achieved their objective, were faced by a new charge from three Ohio regiments. It was only the surprise appearance by Ewell's troops that convinced Tyler to withdraw his men. The Confederates began bombarding the Union troops on the flat lands, with Ewell himself gleefully manning one of the cannons. More Confederate reinforcements began to arrive, including the brigade of Brig. Gen. William B. Taliaferro, and the Union army reluctantly began to withdraw. Jackson remarked to Ewell, "General, he who does not see the hand of God in this is blind, sir, blind."

The impetuosity of Jackson had betrayed him into attacking before his troops were sufficiently massed, which was made difficult by the insufficient means of crossing the river. The Battle of Port Republic had been poorly managed by Jackson and was the most damaging to the Confederates in terms of casualties—816 against a force one half his size (about 6,000 to 3,500). Union casualties were 1,002, with a high percentage representing prisoners. After the dual defeats at Cross Keys and Port Republic, the Union armies retreated, leaving Jackson in control of the upper and middle Shenandoah Valley and freeing his army to reinforce Robert E. Lee before Richmond in the Seven Days Battles.