With Empoli without a victory in their previous 16 league games before Napoli's visit, Luciano Spalletti's side were expected to get the victory that would have seen them keep pace with league leaders Inter Milan.
They were even more overwhelming favourites after a fine finish from Dries Mertens in the first half, and captain Lorenzo Insigne's arrowing effort eight minutes into the second period put them in firm control.
Napoli held the lead until the 80th minute, until they inexplicably left Liam Henderson all alone to get the hosts back in the game, before a goalkeeping howler from Alex Meret let Andrea Pinamonti in to level three minutes later.
The drama, however, was not done there, as Pinamonti slid in at the far post three minutes from time to send the home fans into raptures, and leave Napoli defenders looking at each other wondering how they had thrown this encounter away.
The defeat leaves Napoli third in the standings, without a win in three league games, and five points behind Inter having played a game more. Empoli stay 14th despite that rare victory.