Baxter retained command of his brigade during the reorganization of the Army of the Potomac in March 1864, a sign that he held the confidence of his superiors. His brigade was assigned to the 2nd Division, V Corps, under Maj. Gen. Robinson. At the Battle of the Wilderness, he was shot in the left leg, the bullet also killing his horse. After recuperating, he led a brigade in the 3rd Division, V Corps, during later stages of the siege of Richmond and Petersburg. He was mustered out of the volunteers on August 24, 1865. On May 31, 1866, President Andrew Johnson nominated Baxter for the award of the brevet grade of major general to rank from April 1, 1865 and the U.S. Senate confirmed the award on July 23, 1866.