A hunter discovered the skull in April 2012. Police in Hickory said Thursday the state medical lab in North Carolina and forensic scientists at Marshall University used a DNA profile to identify it, The Charlotte (N.C.) Observer reported.
Zahra and her father, Adam Baker, moved to North Carolina from Australia after he met Elisa Baker online. During her short life, Zahra survived cancer twice, although she lost a leg and became partly deaf.
She vanished in 2010.
Elisa Baker, who pleaded guilty in 2011 and is serving 15 to 18 years in prison, showed investigators where parts of Zahra's body had been concealed.
Adam Baker returned some of Zahra's remains to Australia when he was deported last year.
Hickory Police Chief Tom Adkins said authorities hope to return the rest of her body to her family.
"It brings up the tragedy of Zahra's death and the life she lived before she was killed," Adkins said of the identification. "But it also gives us and the community a sense of finally bringing her home."