The Gaels lost leading scorer Patrick Mills to a right wrist injury late in the first half and Gonzaga took advantage to break a tie for first place in the West Coast Conference.
Mills scored 18 points as Saint Mary's (18-2, 5-1) took a 39-33 halftime lead. With 3 minutes left in the half the sophomore guard sprained the wrist on his shooting hand when he tried to break his fall as went down to the court.
His absence crippled the Gaels' offense as they scored only 23 points in the second half.
Steven Gray added 14 points for Gonzaga (15-4, 6-0), which has won seven straight games.
Diamon Simpson had 17 points and 12 rebounds for Saint Mary's.
The Zags outscored the Gaels 13-6 in the opening minutes of the second half to take a 46-45 lead on Bouldin's driving layup.
After Saint Mary's took a 48-46 lead, the Zags ripped off 12 straight points for a 58-48 lead with 7:49 left and that stood up the rest of the game.
After making seven 3-pointers in the first half, six by Mills, the Gaels made just one in the second.
Gonzaga jumped to a 14-7 lead, but two 3-pointers by Mills brought the Gaels within 16-13. Simpson's dunk gave Saint Mary's a 20-19 lead. Mills hit three 3-pointers in the next 80 seconds to give Saint Mary's a 29-21 lead.
Mills, a native of Australia who played for its Olympic team in Beijing, matched his full-game average of 18 points in the first half, going 6-of-8 from 3-point range. He has scored in double figures in all 20 games this season.