early 15c., "a concommitant symptom;" 1530s, "a secondary signification, that which is included in the meaning of a word besides its primary denotation," from Medieval Latin connotationem (nominative connotatio), noun of action from past-participle stem of connotare "signify in addition to the main meaning," a term in logic, literally "to mark along with," from assimilated form of Latin com "with, together" (see con-) + notare "to mark, note, make a note," from nota "mark, sign, means of recognition" (see note (n.)).
The meaning "that which constitutes the meaning of a word" (1829) originated with James Mill, father of John Stuart Mill, who also developed the use of it.
The use, which I shall make, of the term connotation, needs to be explained. There is a large class of words, which denote two things, both together ; but the one perfectly distinguishable from the other. Of these two things, also, it is observable, that such words express the one, primarily, as it were ; the other, in a way which may be called secondary. Thus, white, in the phrase white horse, denotes two things, the colour, and the horse ; but it denotes the colour primarily, the horse secondarily. We shall find it very convenient, to say, therefore, that it notes the primary, connotes the secondary signification. [James Mill, footnote in "Analysis of the Phenomena of the Human Mind," 1829]