Ramon Dyer had 17 points and Lenny Smith added 16 for the Cougars (15-10, 6-5 Conference USA), who opened the game with a 21-4 run and were never seriously threatened in winning for the third time in four games.
It was another lopsided loss for coach Larry Eustachy in his first season at last-place Southern Miss (10-13, 1-10), which has lost five straight and 11 of 12.
Houston beat the Golden Eagles twice this season, winning the first meeting 63-53 last month behind 19 points from Brian Latham and 18 from Owens.
Owens entered the rematch averaging 17.2 points -- and nearly had that by halftime.
He had just seven points in his last game, a 20-point loss to Charlotte, and more than doubled that in the opening 20 minutes.
Houston led 45-31 at the break, then scored 11 straight points as part of a 17-5 run to open the second half.
Houston shot better than 49 percent from the field and held the Golden Eagles to 34 percent shooting.