1530s, "pointing of the psalms," from Medieval Latin punctuationem (nominative punctuatio) "a marking with points," noun of action from past participle stem of punctuare "to mark with points or dots," from Latin punctus, past participle of pungere "to prick, pierce" (from suffixed form of PIE root *peuk- "to prick"). Meaning "system of inserting pauses in written matter" is recorded from 1660s.

[P]unctuation is cold notation; it is not frustrated speech; it is typographic code. [Robert Bringhurst, "The Elements of Typographic Style," 2004]