The civilian suffered minor injuries in the stabbing at a major crossroads near the Gush Etzion bloc, south of Bethlehem, the army said in a statement.
"Security forces on site overpowered the suspect and transferred her for further medical assistance," the statement said.
Police said in an initial statement that the woman was shot after stabbing a soldier.
The incident came as tensions run high in Israel and the Palestinian territories, after a series of deadly attacks in Jerusalem in November, and the fatal stabbing of an Israeli soldier in Tel Aviv.