The Colombian player underwent arthroscopic surgery to have calcification removed from his right knee.
A statement from Napoli read: "Today's surgery went well and Zuniga will be available in six to eight weeks' time."
The 27-year-old has made four league appearances for Napoli this season.
Napoli will also be without Uruguay defender Miguel Britos for a spell after he dislocated a collarbone in Friday's 2-0 defeat at Roma.
The Uruguay centre-back will be out for 20 days and will miss four Serie A games, including the match at Juventus on November 10.
Napoli are second in the standings, five points behind league leaders Roma, and host Torino on Sunday.