The game began in a peculiar fashion when referee Daniele Doveri injured his shoulder signalling a free kick after just a minute of play.
The contest was held up for seventeen minutes as Doveri received treatment before the fourth official spent ten minutes warming up to take his place.
Uruguayan Cavani found the net after 20 minutes by tucking home following a Blerim Dzemaili through pass.
Cavani continued to be a regular threat and almost made it two from a tight angle moments before Paolo Cannavaro did double the lead from inside the six-yard box.
After the break Cavani was again the main threat for the hosts but he failed to make it three before Andrea Caracciolo could only head wide with a rare chance for Novara.
Napoli next travel to Lecce on Wednesday while Novara host Lazio.