Two physical consequences of the Civil War on the Southern States was the institutional destruction of the system of chattel slavery involving African blacks. Most of the 19th century involved compromises (Missouri and the Great) on the expansion of slavery and many politicians hoped that it would die a natural death as other areas of the country followed the North's industrialization. Following the invention of the cotton gin to make picking easier, the opposite unfortunately occurred and slavery became larger and more profitable than ever. With the servile economy booming, it was clear that it would take a major confrontation to answer this "peculiar institution", and that was the American Civil War.
As the war dragged on, it became clear following Lincoln's reelection that starving the South economically wasn't enough to force their surrender, so Sherman's March to Sea occurred. This was an example of total war in which railroads, farmland, and industry was destroyed to prevent contributions to any sustained war effort, thus severely impacting the ability of the South to wage war. It was harsh but necessary, and it would take years, even with federal aid, to rebuild post-war.
Another physical consequence was the transformation of the social order. It was not just the end of slavery, it was the end of the system and stereotypes (the Southern gentleman, the house and field negro) that had been championed for hundreds of years, leaving much confusion and social disarray. Scalawags were especially offensive, as they were seen to be betrayers of the cause in their cooperation with the Republicans in Congress. A belief in personal victimhood during the unification of the country likely contributed to the development of the Lost Cause movement later in the 19th century. The founding of the KKK during the era of Reconstruction also terrorized and undermined black efforts to assert themselves, more so after the Klan went underground, becoming domestic terrorists.