Australia was in control for most of the contest but could not make it count on the scoreboard with only a four-point lead at half-time.
Croatia then fought back in the third period, tying the game heading into the fourth term as the Crocs looked set for another tight finish.
Hunter Clarke set the tone in the last quarter though, draining a three-pointer for their first basket and while the score was still tied with 6:30 remaining, Clarke again connected from distance to kick-start the game-breaking run.
Kobe Williamson (11 points, six rebounds), Joel Capetola (seven points, four assists, four steals) and Tamuri Wigness (ten points, three steals) all scored as well before Clarke knocked in two more to cap a 12-0 run.
Luke Travers ensured Croatia was not able to answer at the other end of the floor with two rejections and the Crocs held their opponents to just 3-15 shooting overall as they ran out convincing winners.
Clarke's 18 points on 4-7 three-point shooting led four players in double-figures with Australia shooting 46% as a team.
Once again, the combination of Travers (seven points, ten rebounds, three blocks) and Luke Jackson (ten points, 15 boards, two steals) owned the glass and they helped Australia finish with a +14 advantage in rebounds while also restricting Croatia to 29% shooting inside the arc.
Find the box score here.
The Crocs will now take on Turkey, the only team to beat the Aussies through the group stage, in their last game of the Under-17 World Cup in a battle for fifth place in the final standings at 4.30am AEST.