1530s, "pointing of the psalms" (for the purpose of singing them), from Medieval Latin punctuationem (nominative punctuatio) "a marking with points in writing," 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.
The modern system of punctuation was gradually developed after the introduction of printing, primarily through the efforts of Aldus Manutius and his family. ... Long after the use of the present points became established, they were so indiscriminately employed that, if closely followed, they are often a hindrance rather than an aid in reading and understanding the text. There is still much uncertainty and arbitrariness in punctuation, but its chief office is now generally understood to be that of facilitating a clear comprehension of the sense. [Century Dictionary, 1895]
[P]unctuation is cold notation; it is not frustrated speech; it is typographic code. [Robert Bringhurst, "The Elements of Typographic Style," 2004]