Thousands of students were unable to get to school on the buses because of the vandalism, which included smashed windows and broken doors.
Fire extinguishers were also emptied in some of the vehicles.
The teenagers, 17 and 15, face charges of mischief and break and enter.
In all, 24 elementary schools, seven secondary schools and another six private institutions were affected.
The schools did remain open, however, after parents and education authorities jumped into action to get the students to class in Longueuil, south of Montreal.
The buses are expected to be back on the road Monday.