All other players and staff members who underwent tests before Monday's (AEDT) Serie A match against Fiorentina were all negative, the club announced.
Napoli plays Juventus in the Italian Supercup in Reggio Emilio next Thursday (AEDT).
"Unfortunately I have tested positive for COVID," Ruiz said in a statement on Twitter.
"I am isolating at home and following all the protocols set by Napoli and Serie A. I am doing well and so is my family.
"I will be back working with the team when I have fully recovered. Meanwhile I'll continue to support the team from home."
Napoli striker Victor Osimhen has not yet recovered from the virus, having tested positive on his return from Nigeria after the Christmas holidays.