He was commissioned as Lieutenant Colonel for the newly raised 43rd Wisconsin Volunteer Infantry Regiment, serving under Colonel Amasa Cobb. The regiment was assigned to Tennessee, and saw some combat during the Franklin–Nashville Campaign near the end of the war. After the Civil War, Paine returned to Milwaukee and resumed practicing law. During this period, he participated in another significant civil rights case, when he represented Ezekiel Gillespie in the 1866 case of "Gillespie v. Palmer". Gillespie was a former slave who attempted to vote in Milwaukee in 1865, but was turned away. Paine argued that Wisconsin had granted voting rights to African Americans through an 1849 law and referendum, which had been ignored for the previous 17 years. The Wisconsin Supreme Court ruled in Gillespie's favor, ruling that African Americans had the right to vote in Wisconsin. In 1867, Jason Downer, who had succeeded Paine on the Wisconsin Supreme Court, resigned. Wisconsin Governor Lucius Fairchild appointed Paine to fill the vacancy. Paine served on the Supreme Court until his death in January 1871. Paine married Clarissa Wyman. They had five sons, though only three survived infancy. He was an avid reader and enjoyed studying theology. Paine died on January 13, 1871, in Monona, Wisconsin.