A recent drop in form had recently seen Atalanta draw three Serie A games in a row to drop down to third after leading the way at Christmas, but the visit of Napoli gave them an opportunity to cut the gap to the league-leaders.
They looked well-placed to do just that, when the division’s top scorer Mateo Retegui netted his 14th goal of the season courtesy of a fantastic strike into the roof of the net from an angle.
In response, David Neres had a shot saved before the visitors levelled things up shortly before the half-hour mark.
From a similar position, Matteo Politano hammered past Marco Carnesecchi with a fierce strike, leaving the goalkeeper with no chance.
With the momentum now on their side, Antonio Conte’s men were soon in front thanks to another clinical finish, this time from Scott McTominay, who side-footed Andre-Frank Zambo Anguissa's cutback into the top corner from just inside the area.
A quiet start to the second period ensued until Atalanta’s talisman Lookman produced a moment of quality.
Politano had appeared to have prevented any danger, but the Nigeria international adjusted himself to bury into the corner to restore parity once more.
La Dea subsequently went close to going in front, with only a fingertip save from Alex Meret stopping Charles de Ketelaere’s header from nestling in the bottom corner.
Atalanta looked the more likely to find a winner, but the next goal came at the other end as Romelu Lukaku, otherwise quiet, headed Anguissa’s pinpoint cross into the corner.
In true Conte fashion, his side ran down the clock with confidence to prevail and move six points clear at the top.
Inter Milan do have two games in hand to catch them, but their 2-2 draw against Bologna in midweek suggests picking up six points from six is no guarantee.
Atalanta, meanwhile, are now seven points adrift of the Partenopei, and will need to break their current five-game winless run quickly if they want to stay in contention for a maiden Serie A title.