1510s, "refuse, reject," from Middle French réfuter (16c.) and directly from Latin refutare "drive back; rebut, disprove; repress, repel, resist, oppose," from re- "back" (see re-) + *futare "to beat," from PIE root *bhau- "to strike."
Meaning "prove wrong" dates from 1540s. Since c. 1964 linguists have frowned on the subtle shift in meaning towards "to deny," as it is used in connection with allegation. Related: Refuted; refuting.