A statement from European football's governing body said the Serie A club were under investigation for "racist behaviour of supporters, insufficient organisation and the throwing of missiles and/or fireworks".
Tottenham striker Emmanuel Adebayor, who scored his side's away goal in a 4-1 defeat in Thursday's second leg, was allegedly subjected to monkey chants and plastic bananas were waved in one section of the half-empty San Siro.
Tottenham manager Andre Villas-Boas, whose team went through on away goals after the 4-4 aggregate score, told reporters after the game that it was "very easy" to hear the chanting and said he hoped UEFA would act.
Italy had appeared to have finally got to grips with its football racism problem in January when Milan's Kevin-Prince Boateng stormed off the field in a friendly against lower league side Pro Patria following abuse from the stands.
The following week, the government's watchdog for sports events (ONMS) said Italian public security officials will be given the power to stop or interrupt football matches in the case of racist behaviour by fans.
