The Senegal international scored his side's first goal as Maurizio Sarri's men moved four-point clear at the summit of the Italian top-flight log.
Following a barren first half, the 26-year-old put the Partenopei in front after connecting to a Mario Rui cross with a header in the 65th minute.
13 minutes later, Jose Callejon doubled the hosts' lead after he converted Lorenzo Insigne's cross to ensure Napoli's fourth consecutive win.
Koulibaly's latest effort is his fourth this season - highest among defenders in the Serie A - on his 19th appearance for the table-toppers.
The victory guaranteed Napoli retain the top spot regardless of the outcome of the league encounter between second-placed Juventus and Cagliari later on Saturday. They have gathered 51 points from 20 games.