Facundo Roncaglia gave the home team the lead in the 33rd minute when his pass from the half-way line inexplicably bounced over Morgan De Sanctis and into the net.
Napoli equalised before half time through Edinson Cavani's 100th Serie A goal, but Mazzarri felt they deserved to go on to win the game.
"It was an entertaining game and both teams wanted to win," the coach told reporters.
"We were unlucky conceding that shocking goal and perhaps at the end we deserved something more than a point.
"Now we have Parma, who are another tough opponent."
Lazio also dropped points this weekend, meaning Napoli stay in second, five points behind Juventus, but Mazzarri said he wants the team to continue their development despite their great improvement compared to last season.
"We hope to do even better - we may have 13 more points than at this stage last season, but we won’t rest on our laurels."