It was a fourth straight victory for Antonio Conte's side following consecutive losses to Lazio a month ago in the Italian Cup and Serie A.
Atalanta, who ended 2024 in first place level on points with Napoli, aren't playing in Serie A this weekend, competing instead in Saudi Arabia for the Italian Super Cup.
Defending champions Inter Milan, four points back, face city rivals AC Milan in the Super Cup final on Monday, and also won't play in the league until next weekend.
Fiorentina, who've lost three of their last four in the league, remain fifth.
Neres put Napoli ahead near the half-hour mark on Saturday by dribbling between three defenders before unleashing an angled shot with his weaker right foot.
Fiorentina striker Moise Kean then had a potential goal denied for a handball. There was a lengthy VAR review which proved inconclusive, meaning the call on the field stood.
After the break, Lukaku converted a penalty and McTominay drilled in a shot following a defensive error.
Earlier, mid-table Empoli and relegation-threatened Venezia had drawn 1-1 with Joel Pohjanpalo and Sebastiano Esposito trading first-half goals.
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