On the back of their recent unimpressive form, that saw the Parthenopeans fail to win in their last three games, the defender who scored an own goal in their 2-0 defeat to Arsenal in the first leg Europa League quarter-final tie redeemed himself in style at the Stadio Marcantonio Bentegodi.
The 27-year-old opened the scoring for Carlo Ancelotti’s men in the 15th minute after connecting with Dries Mertens’ corner kick.
Arkadiusz Milik doubled the lead in the 64th minute before the Senegal international wrapped up his brace from another set piece with nine minutes left to play.
Bostjan Cesar scored a late consolation for the Yellow and Blues but was not enough to halt their hosts from claiming their 20th win of the season.
Koulibaly featured for the entire duration of the game in his 30th league appearance this season.
Despite the victory, Napoli remain second in the league standings with 67 points from 32 games, 17 points adrift of leaders Juventus who are poised to claim the title.
They will hope to replicate the performance when they host Arsenal in Thursday’s Europa League game.