He was commissioned a brigadier general in the Confederate Army on April 13, 1861, and commanded the forces guarding Georgia's seacoast before being reassigned to Virginia.

His last field service was at the Battle of Antietam (Sharpsburg), where he commanded the division of the wounded Maj. Gen. Richard S. Ewell.

Lawton was seriously wounded early in the morning of September 17, 1862, while defending his portion of the Army of Northern Virginia's line.

Although he brought energy and resourcefulness to the position, he was unable to solve the problem of material shortages and poorly regulated railroads.

In the years after the Civil War, Lawton became increasingly important as a political figure in Georgia, serving in various administrative posts.