"battles among fellow citizens or within a community," from civil in a sense of "occurring among fellow citizens" attested from late 14c. in batayle ciuile "civil battle," etc. The exact phrase civil war is attested from late 15c. (the Latin phrase was bella civicus).
Early use typically was in reference to ancient Rome. Later, in England, to the struggle between Parliament and Charles I (1641-1651); in U.S., to the War of Secession (1861-1865), an application often decried as wholly inaccurate but in use (among other names) in the North during the war and boosted by the use of the term in the popular "Battles and Leaders of the Civil War" series published 1884-87 in "Century Magazine."