Koulibaly was subject to sporadic monkey chants from groups of hardline ultra fans in the Curva Nord section of the San Siro two weeks ago when Napoli lost 2-0.
Serie A officials usually sanction clubs in the days following such incidents but due to a “technical problem” only released details of the punishment on Thursday.
It means a section of the third row of seating at the ground will be closed for Inter's next home game, against Udinese on Saturday, although a repeat of such incidents will “lead to the closure of the entire third row of seating in the stadium”, said a statement.
Inter were also slapped with a €15,000 fine for the supporters' racist behaviour.
It is not the first time Koulibaly has been subject to racism this season.
The towering Senegal international fell victim to monkey chants while playing at Lazio in February, an incident that prompted thousands of Napoli fans to don masks depicting the defender in their following home game.
Meanwhile, Frosinone midfielder Yussif Raman Chibsah will miss three of the season's last four league games after being handed a three-game ban for insulting the referee during a 5-1 defeat to Chievo last weekend that saw the Ghanaian sent off for a second bookable offence.