Tyrone Watson scored 10 points for the Aggies (12-8, 6-2 Western Athletic), who have won six straight games.
LaVanne Pennington had 16 points, four rebounds and five steals for the Spartans (9-9, 3-4).
A 16-2 run over a 6:40 stretch of the first and second halves gave New Mexico State control. Renaldo Dixon ignited the surge with seven consecutive points; meanwhile, San Jose State went scoreless for the last 3:57 of the first half.
Watson's two free throws made it 39-20 with 17:15 remaining, and the Spartans got no closer than 12 points the rest of the way.
The Aggies enjoyed a 46-24 rebounding advantage and outscored San Jose State 22-8 in the paint.
Dixon finished with nine points.