Koulibaly was subjected to monkey noises from sections of crowd during Inter's 1-0 win at the San Siro.
"We asked three times for the match to be suspended," Napoli boss Carlo Ancelotti told Sky after the game.
Koulibaly, 27, was dismissed 10 minutes from time for two bookable offences.
"The player was irritable and he wasn't in the best state of mind," Ancelotti added. "Usually he's a very calm and professional player but there were these noises throughout the game."
The Italian league's sanction will cover Inter's game against Sassuolo on 19 January and the fixture against Bologna on 3 February.
Despite the defeat, Napoli remain second in Serie A with 41 points after 18 games. Juventus, who drew 2-2 at Atalanta on Wednesday afternoon, set the pace with 50 points from their 18 matches. Inter are third with 36 points.
On 29 December, before a three week New Year break, Juventus host Sampdoria while Napoli entertain Bologna. Inter will be at Empoli.