The result moved Benfica to two league-phase wins and left them just one point off the play-off positions going into a decisive double-header against Juventus and Real Madrid.
Mourinho, who earned only his third win in eight meetings with Antonio Conte, praised the intensity and accuracy shown by his players. "We started very well, everything we prepared happened and the players read the game perfectly," he said after the match.
"They played with spirit, cohesion and intelligence. Then they showed class and confidence, and we exploited the spaces we found. Ivanovic caused them so many problems. It is a great win that keeps us in the fight."
Benfica controlled the first half from the first whistle. Napoli came into the match desperate for points after losing both of their away fixtures in this season's competition, but their poor form on the road continued.
Fredrik Aursnes twice missed clear chances inside the opening 20 minutes, first denied by Vanja Milinkovic-Savic and moments later dragging a shot wide with the goal open. Franjo Ivanovic also curled narrowly past the post as Benfica pressed relentlessly.
The breakthrough arrived midway through the first half when Ivanovic rose to nod a lofted delivery into the path of Richard Rios, who reacted sharply to steer the ball into the net. Napoli responded with a brief spell of pressure, but Giovanni Di Lorenzo headed wide from Noa Lang's cross before Nicolás Otamendi fired off target just before the break.
Conte made a double change at half-time, introducing Leonardo Spinazzola and Matteo Politano, but Benfica struck again within five minutes. After dealing with a Napoli corner, goalkeeper Anatoliy Trubin launched a rapid transition, and Rios threaded a clever pass to the near post where Leandro Barreiro finished with an outstanding back-heel flick to make it 2-0.
Napoli rarely threatened, testing Trubin only in the 71st minute when David Neres forced a strong save from distance. Benfica nearly added a third as Vangelis Pavlidis twice saw efforts stopped by Milinkovic-Savic, but Mourinho's side closed out the match comfortably.
With Juventus and Real Madrid still to come, Mourinho has admitted the challenge ahead is "extremely tough," but he insisted Benfica remain fully alive in the competition. "We are still in it," he said. "This win gives us belief, and the players know exactly what is needed now."
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