Cavanaugh finishes with 170 wins, the most in school history.
He led his program to 19 winning seasons, shares of three Northeast-10 Conference titles, and four consecutive NCAA championship appearances between 2005 and '08.
He also coached four players who went on to careers in the NFL: offensive lineman Joe Andruzzi; tight end Travis Tucker and defensive ends Jacques Cesaire and Scott Mersereau.
The Owls finished this season 3-8.
The school says it will immediately begin a national search for his successor.