Fr John Ssenyondo had been missing since being kidnapped by gunmen six months ago.
His car was blocked by unknown attackers who then forced him into their vehicle on April 30.
Police found the mass grave whilst looking for 43 student teachers who went missing at the end of September.
A group of civilian community police look at the excavated grave.
Officers have now revealed the bodies found in the grave near the town of Ocotitlan were not the students.
Dental records and DNA had to be used to identify Fr Ssenyondo, who had been in Mexico for five years.
Revd Victor Aguilar, vicar in the diocese of Chilpancingo-Chilapa, told the BBC: "We don't know the motive, you know violence is widespread in the state."