1520s, "to sully or stain" (the reputation, character, etc.), from Latin denigratus, past participle of denigrare "to blacken; to defame," from de- "completely" (see de-) + nigr-, stem of niger "black" (see Negro), which is of unknown origin.
The figurative sense is oldest in English; the literal sense of "blacken, make black" is recorded from 1620s. But denigrate as a past-participle adjective meaning "darkened, discolored" is attested from early 15c. "Apparently disused in 18th c. and revived in 19th c." [OED]. Related: Denigrated; denigrating.