It was the second time in the match they had used flares, with some being thrown on during the first half as well - with the match interrupted for three minutes after Croatia scored.
Antonio Candreva had opened the scoring for Italy before Ivan Perisic equalised just four minutes later. The match eventually finished 1-1.
Former Croatia boss Slaven Bilic said: 'It's (crowd trouble and flares being thrown) a big problem, not only in Croatia but definitely there.'
The game itself was a pacey first-half which only slowed with the interruptions for the flares.
This match will unfortunately be remembered for the ugly scenes caused by the visiting supporters, however.
