Referee Bjorn Kuipers escorted the players from the field at San Siro during the longest delay towards the end of the second half, as flares rained down onto the playing surface.
Trouble appeared to break out in the area of the ground housing visiting supporters while the game was suspended, but play was able to resume.
Both teams came into Sunday's match, which had been threatened by heavy rain in Milan, boasting maximum points in Group H.
Antonio Candreva gave Italy an 11th-minute lead when he drove home from distance to beat Danijel Subasic as Croatia conceded for the first time in qualifying.
However, a rare error from the experienced Gianluigi Buffon enabled Ivan Perisic to equalise with a low strike just four minutes later.
Croatia created the better chances thereafter, despite losing Luka Modric to injury later in the first half.
Elsewhere in the group, Havard Nordtveit was the match-winner for Norway as they moved within a point of Italy and Croatia with a 1-0 away victory against Azerbaijan.
Malta scored their first goal of the campaign to come from behind and earn a memorable 1-1 draw in Bulgaria, leaving only San Marino and Gibraltar yet to find the net in qualifying.
Netherlands eased the pressure on head coach Guus Hiddink by strolling to a 6-0 victory over Latvia in Group A.
The Dutch had won just one of their opening three fixtures, prompting Hiddink to suggest he would leave the role if his side did not beat Latvia, but goals from Robin van Persie, Arjen Robben and Klaas-Jan Huntelaar saw them three up at the break.
Jeffrey Bruma made it 4-0 12 minutes from time, before further goals from Robben and Huntelaar completed the rout.
The Czech Republic continue to hog the limelight in Group A, having maintained their 100 per cent start by coming from behind to beat Iceland.
Iceland, who also came into the fixture having won their opening three qualifiers, went ahead through Ragnar Sigurdsson, but Pavel Kaderabek levelled in first-half stoppage time.
The match was settled when goalkeeper Hannes Halldorsson scored an own goal shortly after the hour mark.
Turkey climbed to fourth in the group with their first win of the campaign - a 3-1 triumph at home to Kazakhstan.
Israel climbed above Wales to sit top of Group B courtesy of an impressive 3-0 victory over Bosnia-Herzegovina, with Chris Coleman's men earning a hard-fought goalless draw in Belgium.
Cyprus thumped Andorra 5-0 in the group's remaining match.
