1630s, "to point out," from Medieval Latin punctuatus, past participle of punctuare, from Latin punctus, past participle of pungere "to prick, pierce" (from suffixed form of PIE root *peuk- "to prick").
Meaning in reference to text, "to have pauses or stops indicated," is from 1818, probably a back-formation from punctuation. Hence, "interrupted at intervals" (1833). Related: Punctuated; punctuating.