France forward Benzema had not scored since fifteen December however completed the scoring against the second-tier side once coming on as a substitute.
The 19-time winners led 2-0 once goals by Raphael Varane and Lucas Vazquez.
Nineteen-year-old Brazil forward Vinicius Junior added the third before Benzema’s goal.
Joining Real Madrid within the last eight are holders Valencia, Athletic Bilbao, Villarreal, Granada and Real Sociedad.
Barcelona face Leganes within the competition on Thursday, whereas Sevilla are at second-tier Mirandes a similar night.