On June 29, the bulk of McClellan's army concentrated around Savage's Station on the Richmond and York River Railroad, a Federal supply depot since just before Seven Pines, preparing for a difficult crossing through and around White Oak Swamp. It did so without centralized direction because McClellan had personally moved south to Malvern Hill after the battle of Gaines' Mill without leaving directions for corps movements during the retreat nor naming a second in command. Clouds of black smoke filled the air as the Union troops were ordered to burn anything they could not carry. Union morale plummeted, particularly for those wounded, who realized that they were not being evacuated from Savage's Station with the rest of the Army.
Lee devised a complex plan to pursue and destroy McClellan's army. Longstreet's and A.P. Hill's divisions looped back toward Richmond and then southeast to the crossroads at Glendale, Holmes's division headed farther south, to the vicinity of Malvern Hill, and Magruder's division was ordered to move due east to attack the Federal rear guard. Stonewall Jackson, commanding three divisions, was to rebuild a bridge over the Chickahominy and head due south to Savage's Station, where he would link up with Magruder and deliver a strong blow that might cause the Union Army to turn around and fight during its retreat. McClellan's rear guard at Savage's Station consisted five divisions from Sumner's II Corps, Heintzelman's III Corps, and Franklin's VI Corps. McClellan considered his senior corps commander, Sumner, to be incompetent, so he appointed no one to command the rear guard.
Initial contact between the armies occurred at 9 a.m. on June 29, a four-regiment fight about two miles west of Savage's Station, lasting for about two hours before disengaging. Meanwhile, Jackson was not advancing as Lee had planned. He was taking time to rebuild bridges over the Chickahominy and he received a garbled order from Lee's chief of staff that made him believe he should stay north of the river and guard the crossings. These failures of the Confederate plan were being matched on the Union side, however. Heintzelman decided on his own that his corps was not needed to defend Savage's Station, so he decided to follow the rest of the army without informing his fellow generals.
Magruder was faced with the problem of attacking Sumner's 26,600 men with his own 14,000. He hesitated until 5 p.m., when he sent only two and a half brigades forward. Union artillery opened fire and pickets were sent forward to meet the assault. The two brigade front of Kershaw and Semmes began to push the narrow defensive line of one of Sedgwick's brigades. Sumner managed this part of the battle erratically, selecting regiments for combat from multiple brigades almost at random. By the time all of these units reached the front, the two sides were at rough parity — two brigades each. Although Magruder had been conservative about his attack, Sumner was even more so. Of the 26 regiments he had in his corps, only 10 were engaged at Savage's Station.
The fighting turned into a bloody stalemate as darkness fell and strong thunderstorms began to move in. The "Land Merrimack" — the first instance of an armored railroad battery to be used in combat — bombarded the Union front, with some of its shells reaching as far as the field hospital at the rear. The final action of the evening was as the Vermont Brigade, attempting to hold the flank south of the Williamsburg Road, charged into the woods and were met with murderous fire, suffering more casualties than any brigade on the field that day.
There were about 1,500 casualties on both sides, plus 2,500 previously wounded Union soldiers who were left to be captured when their field hospital was evacuated. Stonewall Jackson eventually crossed the river by about 2:30 a.m. on June 30, but it was too late to crush the Union Army, as Lee had hoped. General Lee reprimanded Magruder, but the fault for the lost opportunity must be shared equally with the poor staff work at Lee's own headquarters and a less than aggressive performance by Jackson.