The 57-year-old former Sampdoria striker has been a key figure in establishing the Verona outfit in the Italian top flight.
He has now decided to step down, although club president Luca Campedelli has left the door open for a potential return.
Campedelli is quoted as saying on the club's official website: "Words are not enough to explain how important and crucial you have been for me.
"This is not goodbye but an arrivederci. See you soon."
Chievo finished 16th in Serie A last season.