The remains were discovered last week in the residence where Steven King, the ex-boyfriend of Elaina's mother, Angela Steinfurth, used to live.
Initial autopsy results were inconclusive, but police said in a press release Tuesday that DNA tests confirmed the identity of the skeletal remains.
Baby Elaina's mother told police on June 2 the toddler had disappeared after she put her down for a nap in King's house.
Authorities, who had conducted a previous search of the garage, said the remains were not found early in the investigation because the garage was very difficult to search and they were not able to bring the cadaver dogs inside.
Both King and Steinfurth have been indicted on obstruction of justice charges for allegedly providing false information in the case. Both have pleaded not guilty.
Police have not elaborated on what new information prompted them to conduct a second search of the garage.