Success on the fields of Second Manassas had made Robert E. Lee bold. In addition to advancing his army into Maryland, Lee divided his invasion force and sent a large portion of it to seize the Federal arsenal at Harpers Ferry. His opponent, Gen. George B. McClellan however, was given a mislaid copy of one of Lee’s orders that revealed Virginian's plans and troop positions. Aware that a portion of Lee's army was now vulnerable to attack, McClellan advanced on South Mountain.

Only a small Confederate force under D. H. Hill protected Turner's and Fox's Gaps, two vital passes through the South Mountain range. Early on September 14, Gen. Jacob D. Cox's division of the Union Ninth Corps launched an attack against Samuel Garland's brigade at Fox's Gap. Cox's 3,000 Ohioans overran Garland's North Carolinians, driving the southerners from behind a stone wall and mortally wounding Gen. Garland. With Fox's Gap all but clear, Cox awaited reinforcements to further his gains.

Support, however, was not forthcoming. Despite having the strategic and numerical advantage over his opponent—or perhaps because of it—a spirit of leisure seemed to pervade McClellan's headquarters, where the commanding general determined to let his subordinates direct the unfolding battle. Making matters worse, the usually aggressive Ninth Corps head, Gen. Jesse L. Reno, was slow to send reinforcements to Fox's Gap, thus allowing additional troops from Gen. James Longstreet's command to shore up the Confederate positions on South Mountain. Burnside, in turn, chose to wait for the arrival of Joseph Hooker's First Corps before making a concerted effort to seize the mountain passes. An uncoordinated Confederate counterattack foundered in the region's confusing thickets. By now, both sides had received reinforcements as the battle for control of South Mountain escalated.

While Union and Confederate commanders funneled troops into Fox's and Turner's Gaps, excessive caution plagued Gen. William B. Franklin's Federal Sixth Corps on its way to relieve the besieged garrison at Harpers Ferry. Roughly one thousand Confederates held Crampton's Gap, yet Franklin was convinced the Rebels were in strong enough force to delay the advance of his 12,000-man corps. Gen. Henry W. Slocum, however, felt differently. At around 4 p.m., Slocum's division of New Jersey, New York, and Pennsylvania troops charged headlong up the slope and into Crampton's Gap, dislodging the outnumbered Confederates from the protection of a stone fence. Even the arrival of two Georgia regiments under Howell Cobb did little to stem the Union tide. A second attack drove the remaining Confederates down the western slope of South Mountain, leaving the Sixth Corps in possession of Crampton's Gap. But with daylight fading and Confederate reinforcements forming in the distance Franklin halted his column.

Meanwhile, at Turner's Gap, Hooker's corps had arrived on the field and Burnside was finally ready to launch a coordinated assault. At 4 p.m.—seven hours after the fighting began—Union divisions under generals George Meade and John P. Hatch made a relentless charge on the northern end of Turner's Gap. The brunt of the Federal onslaught fell upon the 1,200 men of Robert Rodes’ brigade , whose regiments suffered severe casualties during the struggle. Meade's Pennsylvania Reserves' well-directed attack pressed the Confederates' left flank while Hatch's troops advanced on their right. Only the timely arrival of reinforcements from Longstreet prevented the Confederate line from collapsing. After a brutal firefight along a cornfield fence, Hatch broke through the Rebel line but darkness prevented the capture of Turner's Gap.

Back at Fox's Gap, the reunited Ninth Corps mounted a separate effort to seize control of Turner's Gap but ran into stiff resistance from Confederate divisions under generals John B. Hood and D. H. Hill. Casualties mounted, among them Gen. Reno, who was shot down in almost the same spot as Samuel Garland had been that morning. A diversionary attack by Gen. John Gibbon's "Black Hat Brigade" produced only more bloodshed. As the sun set over South Mountain, the exhausted Confederates still maintained control of Turner's Gap.

Though Lee, Longstreet, and D. H. Hill agreed to abandon South Mountain before daylight on September 15, the bloody, day-long struggle, bought the Confederate army valuable time to consolidate its position—and ready itself for the coming battle along Antietam Creek. McClellan had lost his best chance of destroying Lee's army in detail.