Edinson Cavani got the ball rolling for the hosts after 21 minutes after Alberto Fontana made a hash of clearing Ivan Radovanovic's looping back pass.
Paolo Cannavaro coolly added a second soon after, as both goals came during the opening half.
Following a lengthy delay at the start of the match after referee Daniele Doveri had to be taken off with an apparent shoulder injury and replaced by fourth official Gennaro Palazzino, Napoli set to work on overcoming their struggling opponents.
Yet the hosts made tough work of that task early on as Cavani smashed the ball wide of the Novara goal from just a few yards out in the 10th minute, having been teed up by Christian Maggio.
It was roles reversed just five minutes later as a Cavani corner was powerfully met by the head of the unmarked Maggio - only for the Napoli faithful to see Giuseppe Gemiti expertly clear his goal-bound effort off the line.
In between those moments of Napoli pressure, Novara did threaten with Giuseppe Mascara clipping the ball through to Filippo Porcari, which prompted Morgan De Sanctis to quickly come off his line to deny any strike at goal.
But it was to prove to be only a brief respite for the visitors as, just past the 20-minute mark, an error from Novara keeper Alberto Fontana gifted the ball to Blerim Dzemaili who fed Cavani with the Uruguayan striker atoning for his earlier miss and putting Napoli in front.
Walter Mazzari's men were continually finding pockets of space as they imposed themselves on the game and pinned Novara back.
It came as little surprise that a second followed five minutes before the interval. A long ball hit over the top by Walter Gargano was collected by Cavani whose curling effort, although well parried by Fontana, fell directly into the path of Cannavaro, who sidefooted home with aplomb.
Novara remained on the back foot - and camped in their own half - for the majority of the second 45 minutes, as the movement and link-up play between Dzemaili, Cavani, Marek Hamsik and Maggio continued to cause the visitors all sorts of problems.
However, De Sanctis was called on to save Andrea Carraciolo's headed attempt towards the end, as well as remain big in knocking the ball away from the on-rushing Novara striker moments afterwards.
Of Napoli's various chances, Hamsik came closest with a curling effort on 80 minutes, from which Fontana had to get down low to expertly parry the ball to safety.
While they were unable to add to their two-goal lead secured since half-time, Napoli always had an element of control to their play, with the win potentially coming at a crucial time for their end of season exploits.
The victory sees Napoli move up to fifth in the standings - just three points behind third-placed Lazio in the race for Champions League qualification - while Novara's swift return to Serie B looks increasingly likely as they remain 11 points adrift of safety.