At a news conference in Woodstock, Ontario Provincial Police officials said the decomposed remains found in a rural farm area Sunday were those of Victoria Stafford.
She was last seen in a security video leaving school with a young woman April 8.
The Canwest News Service said court documents show police suspect the girl known as Tori was killed within 24 hours of her abduction.
More than 100 police officers from the Oxford Community Police and OPP worked on the search and investigation, which led to the arrests of Michael Rafferty, 28, and Terri-Lynne McClintic, 19, May 19 on kidnapping and first-degree murder charges.
Police will not say what led to the arrests so as not to jeopardize prosecution. They said they notified the girl's parents Monday night of the pathologist's findings.
Detective-Inspector Bill Renton told reporters forensic work is continuing and the telephone tip line for investigators will remain open.
Trials for the accused aren't expected to begin until next year, report said.
Putin thinks Obama would save him if he were drowning
Justin Bieber crashes Drake Bell's album release party