A medical examiner said Matula, 24, had been shot in the head, the Minneapolis Star Tribune reported.
Police discovered the body Saturday in Mississippi River Park near Sartell and about 60 miles northwest of Minneapolis. They were led to the burial site by a Boy Scout leader who found a piece of fabric sticking out of the ground while on a solo hike.
Eden Praire Police Chief Rob Reynolds told the Star Tribune investigators were certain Matula was killed by her ex-boyfriend, David Roe, 24. Roe shot himself outside police headquarters in the Minneapolis suburb after being questioned the day after Matula disappeared.
Roe told investigators Matula got out of his car while they were talking in a park and he did not know what happened to her. But area residents reported hearing what sounded like gunfire early May 2 in the parking lot of a Lutheran church, and police found one bullet on the ground there.
"Tonight our every thought is with the Matula family," Reynolds said. "I believe for us and the community it is a sense of relief. Mandy was very popular in the city, so it's something that affects the entire community."
Police said they found Matula's class ring and the logo of her University of Minnesota-Duluth fast-pitch softball team with the skeletal remains.
Beyonce flaunts bikini body, Blue Ivy in vacation pics
Gal Gadot cast as Wonder Woman for 'Batman vs. Superman'