It happened at a home on Lick Mill Boulevard.
Investigators say the woman called police Sunday afternoon threatening to harm herself and others.
When officers arrived at the home, they say she attacked them with an aluminum baseball bat and the officers fired.
Sergeant Alan Wolf and Officer Andrew McGuire are currently on paid administration leave, while the police department investigates the incident.
Police have not released the woman's name at this time.
This has been the first officer-involved shooting for the Santa Clara Police Department this year.