"to mark or blot out as with a pen, erase (words), obliterate," c. 1600, from Latin expungere "prick out, blot out, mark (a name on a list) for deletion" by pricking dots above or below it, literally "prick out," from ex "out" (see ex-) + pungere "to prick, pierce" (from suffixed form of PIE root *peuk- "to prick").
According to OED, taken by early lexicographers in English to "denote actual obliteration by pricking;" it adds that the sense probably was influenced by sponge (v.). Related: Expunged; expunging; expungible. In U.S. history, the Expunging Resolution was adopted by the Senate in 1837 to expunge from its journal a resolution passed by it in 1834 censuring President Jackson.