The Worcester County (Mass.) District Attorney's office said Jeremiah's body was found "wrapped in a blanket-type object" in a "suitcase, duffle bag-type material" roughly 40 feet off Route 190 Friday morning.
"It appears to be a homicide," District Attorney Joe Early said.
"The autopsy report is not complete," Early added Saturday, after confirming Jeremiah's identification.
"I am so grateful to the State Police and others in law enforcement for their tenacity in finding Jeremiah, and so sad that he was not found alive," Massachusetts Gov. Deval Patrick said. "We now look to the District Attorney to prosecute this crime to the fullest extent of the law."
Jeremiah, of Fitchburg, was reported missing in December, though officials say he appeared to have disappeared in September.
His mother, Elsa Oliver, and her boyfriend, Alberto Sierra, were indicted on charges of assaulting and kidnapping the boy.