The Italian side will also play a third match at the San Siro without opening the 'curva' section of the ground, popular with fans known as 'ultras'.
Napoli boss Carlo Ancelotti said he asked for the match to be suspended three times and that Koulibaly was targeted in the 1-0 defeat.
Inter are deciding whether to appeal.
A supporter who was with a group of Inter Milan fans died after being knocked down by a van amid violence before the match in Milan.
Four Napoli fans were hurt and one of them was stabbed, police said.
Inter's next three home league games are against Sassuolo on 19 January, Bologna on 3 February and Sampdoria on 17 February.
In addition to the punishment for Inter, Serie A have given Koulibaly a two-match ban after the Senegal international was sent off.
The 27-year-old received two yellow cards in a matter of seconds in the 80th minute. The first was for a foul on Matteo Politano, the second for sarcastically applauding the referee's decision.
Read More (...)