Wheaton remained in command of the brigade during Lt. Gen. Ulysses S. Grant's Overland Campaign in 1864, as well as during the subsequent Siege of Petersburg. His men were hurried by train to Washington, D.C., in time to help repel Jubal Early's raid on the capital. During the ensuing operations in the Shenandoah Valley, under Maj. Gen. Philip Sheridan, Wheaton was promoted to command of the first division after Brig. Gen. David Allen Russell was killed at the Third Battle of Winchester. His division fought well in subsequent battles. In the Battle of Sailors Creek Virginia, on April 6, 1865, his division captured Confederate Major General George Washington Custis Lee, son of Robert E. Lee. After the return of VI Corps to the Petersburg front, Wheaton earned the brevet rank of major general in the volunteer army and was brevetted colonel in the regular services.