Gomez was replaced after 72 minutes of the 1-0 victory at the Stadio San Paolo and the Germany international underwent tests on the injury on Monday.
Following the results of those tests Fiorentina announced the 28-year-old would be sidelined for a week - meaning he would miss Wednesday's visit of Milan and Sunday's trip to Samp - before undergoing further scans.
A statement on Fiorentina's official website read: "Mario Gomez underwent diagnostic procedures today after injuring his knee in yesterday's league match against Napoli.
"Scans revealed a Grade I sprain of the medial collateral ligament. The striker will rest for a week while having appropriate treatment before having further tests and scans."
Gomez, a 20million euro signing from Bayern Munich last summer, was ruled out for five months earlier this season after suffering a knee ligament injury during a match against Cagliari in September.
Fiorentina's win on Sunday saw them move to within seven points of third-placed Napoli in the Serie A standings.