The hosts opened the scoring through Antonio Candreva, before Ivan Perisic pulled Croatia level in the 15th minute, with flares subsequently being hurled onto the pitch.
Further flares were then lit and thrown onto the playing surface shortly after the 70-minute mark, before trouble appeared to break out in the area of the ground housing visiting fans.
The match was restarted after a delay of around 10 minutes, but neither side could find a winner.
UEFA subsequently opened an investigation into the incidents and, on Friday, ordered Croatia to close an area of Stadion Maksimir comprising 8,000 seats for their next home qualifier against Norway in March.
The Croatian Football Federation has also been fined €80,000 for offences including racist behaviour and crowd disturbances.
Italy, meanwhile, have been hit with a €13,000 penalty for the setting off of fireworks.
