Dubois went missing February 13, 2009, while walking to Escondido High School.
Crews drained a pond Saturday in search of Dubois after a woman reported her children found what looked like human hair in a nearby park. Authorities said the search turned up no clues.
Maher did not elaborate on what details led to the discovery of Dubois's bones.
Pala is in northern San Diego County, about 25 miles from Escondido.
Investigators suspect that Dubois may be a victim of registered sex offender John Albert Gardner. Gardner was arrested last week in the death of 17-year-old Chelsea King, who was found in a shallow grave along the south shore of Lake Hodges.
Gardner was a registered sex offender for a 2-year period. He spent five years in prison for sexually assaulting a 13-year-old girl in 2000.