Brazil star striker Neymar was kneed in the back by Zuniga during their quarter-final on Friday and suffered a fractured vertebra that has ruled him out for the remainder of the tournament.
Zuniga has come under fire for the incident, while Brazil's football federation the CBF had pushed for disciplinary action against the 28-year-old - who did not receive a card for the challenge - but that was rejected by FIFA's disciplinary committee who said the referee had seen the incident.
Napoli on Tuesday issued a statement in support of their player, saying: "Napoli are sorry for the accident that occurred that will prevent Neymar from playing in the semi-final against Germany.
"For the Brazilian champion we send our best wishes for a speedy recovery.
"At the same time, the club expresses its support for Zuniga , who has been subjected to fierce criticism and threats of all kinds, for a foul in play that was not malicious but unfortunate in its consequences.
"We note with relief that, in addition to the referee and his assistants, FIFA's disciplinary committee stated that there were no bad intentions on Zuniga's part."
Neymar will be sidelined for at least four weeks.
Brazil play Germany in Tuesday's semi-final in Belo Horizonte.