Dwayne Davis and Jerrold Brooks had 11 points each for the Eagles (12-4, 1-0 Conference USA), who shot 69.6 percent (32 of 46) from the floor.
Austin Ramljak scored 14 points and Tamir Jackson 13 for the Owls (3-11, 0-1).
Southern Miss scored the contest's first seven points and never trailed. Rice was still within shouting distance, trailing 38-27 early in the second half, but a scoreless stretch of 4:48 by the Owls ended the competitive phase of the game.
Southern Miss outrebounded Rice 32-16 and enjoyed a 46-20 scoring advantage in the paint.
Boardingham had seven rebounds.