A hattrick by Arkadiusz Milik and Dries Mertens penalty was more than enough to ensure the Partenopei finished in second place in Group E, behind Liverpool who beat Red Bull Salzburg 2-0.
"When on the field, we always give our best. This is an important victory," Koulibaly posted on Twitter.
Koulibaly has been ever-present for Napoli on the European scene this season, racking up a total of 540 minutes.
The 28-year-old has averaged 75.2 touches in the Champions League this season, 48.5 accurate passes per game (83%), as well as 1.5 interceptions, 2.2 tackles, 5.2 clearances, 3.7 ground duels won (59.5%) and 2.3 aerial duels won (66.7%).