The versatile Panathinaikos full-back is due to feature at his first FIFA World Cup in Brazil, having made his only qualifying appearances in the play-off win over Iceland.
However, the 32-year-old, who picked up the injury in the recent friendly victory over Australia, will now undergo treatment, leaving coach Niko Kovac sweating on his fitness for the competition.
"Danijel Pranjic has a left ankle sprain and will undergo treatment during the upcoming days," said the Croatian Football Federation via their official Twitter account.
Croatia have won both their World Cup warm-ups against Mali and Australia as they prepare for their opener against hosts Brazil on Thursday.
However, Kovac was less than impressed by Australia's approach to the fixture, stating he "didn't think (the game) was a friendly encounter".
Following their Group A opener against Brazil, Croatia take on Cameroon and Mexico as they look to reach the knockout stage for the first time since their tournament debut in 1998.
