late 14c., "relating to civil law or life; pertaining to the internal affairs of a state," from Old French civil "civil, relating to civil law" (13c.) and directly from Latin civilis "relating to a citizen, relating to public life, befitting a citizen," hence by extension "popular, affable, courteous;" alternative adjectival derivation of civis "townsman" (see city).
The sense of "polite" was in classical Latin, from the courteous manners of citizens, as opposed to those of soldiers. But English did not pick up this nuance of the word until late 16c. "Courteous is thus more commonly said of superiors, civil of inferiors, since it implies or suggests the possibility of incivility or rudeness" [OED]. Civil case (as opposed to criminal) is recorded from 1610s. Civil liberty is by 1640s. Civil service is from 1772, originally in reference to the East India Company.