The Serie A side earned their first victory in the Champions League this season, courtesy of first-half goals from their two influential attacking players
The Italian club took the lead in the 15th minute through Marek Hamsik's fine strike before Edinson Cavani converted a penalty two minutes later to ensure Walter Mazzarri's men earned their first victory in Europe this season.
Despite a nervous start, the home side came close to opening the scoring on 12 minutes. Cavani's shot from the edge of the box was well blocked by Mateo Musacchio. However, the ball fell to Ezequiel Lavezzi who saw his powerful effort narrowly miss the top corner.
Two minutes later, Mazzarri's men were ahead courtesy of Hamsik's smart finish. The Slovakian midfielder peeled off his marker to receive Lavezzi's ball over the top of the Villarreal defence. Hamsik controlled the ball before smashing it into the far corner from a tight angle.
On 17 minutes, the Italian club doubled their lead after Gonzalo Rodriguez had clumsily brought down Lavezzi in the penalty area. Cavani, who has scored Napoli's equaliser in the 1-1 draw against Manchester City in matchday one stepped up, successfully sending Diego Lopez the wrong way to leave Villarreal in big trouble.
Despite being 2-0 down, the away side started the second-half positively and nearly grabbed a goal back on 50 minutes. Substitute Javier Camunas pinged an inviting cross into the box which was met by the head of Giuseppe Rossi. However, the Italy international could only watch on as his effort was well saved by Morgan De Sanctis in the Napoli goal.
Villarreal continued their fight to get back into the game but struggled to create chances against a sturdy Napoli backline. Their frustrations were summed up in the 75th minute when Camunas blasted his shot over the bar, despite turning past Juan Camilo Zuniga in the area.
The Spanish side carried on in their search for the goal that would give them hope of getting back into the game yet Mazzarri's side stood strong to earn all three points.
Napoli currently sit in second place in their group, while Villarreal are in danger of an early exit, sitting at the bottom and yet to pick up a point.
Next up for Napoli in the Champions League is a home encounter against Bayern Munich on October 18 while Villarreal travel to Manchester City on the same evening.