Flares and fireworks were thrown onto the pitch shortly after Ivan Perisic's goal in the 15th minute cancelled out Antonio Candreva's opener in the Group H fixture that finished 1-1 at San Siro.
Play was then briefly suspended shortly after the 70-minute mark when further flares were launched at the field, before trouble appeared to break out in the area of the ground housing visiting fans.
The match was restarted after an approximate 10-minute delay, but neither side could find a winner.
UEFA will now investigate both teams for setting off fireworks, while Croatia are also under review for alleged incidents of racism from supporters.
"Disciplinary proceedings have been opened following the European Qualifier Group H match between Italy and Croatia, played on 16 November in Milan," read a statement from UEFA.
UEFA's Control, Ethics and Disciplinary Body is set to deal with the case on December 11.
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