Croatia, helped by a mistake by veteran goal-keeper Gianluigi Buffon, held Italy to a 1-1 away draw but their evening was ruined by their fans who twice interrupted play by throwing flares onto the pitch.
Police arrested 16 Croatia fans on Monday morning.
The contingent of around 5,000 Croatia fans stopped play for around three minutes after their team's equaliser in the first half of the Euro 2016 qualifier. Both teams have 10 points from four games and top Group H.
The second incident was more serious and the players were led off the field for 10 minutes as more flares landed on the field, filling the San Siro stadium with smoke.
Television pictures showed Croatia fans clashing with riot police who tried to quell the trouble.
"It's not the first time and it's not accidental. I hope the bodies in charge will find a way to solve the problem because it paints a bad picture of Croatia," said coach Niko Kovac. "I was ashamed and I apologised to the Italians after the game. There were families with children up there."
At one point, it seemed there could be a repetition of the Euro qualifier in 2010 when Italy's match against Serbia in Genoa was called off after seven minutes because of crowd trouble caused by visiting fans.
In 2005, a Champions League tie between rivals AC Milan and Inter Milan at San Siro was abandoned in the second half when Inter fans threw flares onto the field.