"Sorry to announce that I had to withdraw from the Australian Open with a lower back stress fracture," the 24-year-old said in a post on her Twitter account.
"Going back home, will miss my Aussie fans!"
The world number 10 suffered a knee injury in October, but returned to play her first WTA tournament at Brisbane last week where she made the quarter-finals.
She was dumped out of the Sydney International in the second round on Tuesday by Pole Agnieszka Radwanska in straight sets.
Bosnia-born Petkovic, famous on tour for her post-match victory dances, upset Maria Sharapova on the way to the quarter-finals at Melbourne Park last year where she was stopped by eventual finalist Li Na.
The 10th seed's withdrawal came shortly after seven-times Grand Slam winner Venus Williams pulled out, also citing health reasons.
Williams has been receiving treatment for Sjogren's syndrome, an auto-immune disease that causes fatigue and joint soreness.
A number of other contenders in the women's draw head into the year's first Grand Slam under injury clouds, including champion Kim Clijsters with a strained hip muscle, and fellow former world number one Serena Williams, who twisted her ankle in Brisbane last week.
- Related links