Kam McLeod, 19, and Bryer Schmegelsky, 18, have been on the run since late July when three bodies, including those of an Australian-US couple, were found in northern British Columbia.
The teenagers were later seen 3,300km (2,050 miles) to the east, in Manitoba, where police concentrated their search.
The two bodies were found near the town of Gillam on Wednesday.
"Hopefully this will help the families of the victims achieve a sense of closure," said federal Public Safety Minister Ralph Goodale.
