The Golden Eagles (5-2) forced 13 of New Mexico State’s 19 turnovers in the first half and led 40-26 at intermission.
The Aggies (5-3) cut it to seven, 69-62, late in the second half but Neil Watson of Southern Miss went 5 of 7 from the free throw line in the final 1:01.
LaShay Page added 16 points and Watson finished with 15, including 7-for-9 shooting from the foul line, for the Golden Eagles.
It was the second time in eight days Southern Miss beat the Aggies, the first an 80-72 win in the semifinals of the Great Alaska Shootout on Nov. 25.
New Mexico State was by Christian Kabongo with 21 points on Sunday. Wendell McKines added 15 points, including his career 1,000th on his first field goal of the game for the Aggies.