Jordan Ford led the Gaels (20-5, 7-3 West Coast Conference) with 19 points and a career-high six assists.
Braun Hartfield scored 18 points with five rebounds and five assists for the Toreros (8-17, 1-9), who have lost four straight.
Neither team managed a double-figure lead and for the most part the game was even. Saint Mary's made just 1 of 15 3-point attempts and shot 39% overall but made 21 of 28 free throws. San Diego shot 44% with four 3-pointers but was only 12 of 23 from the line.
Saint Mary's is home against No. 2 Gonzaga on Saturday. San Diego is home against Portland.
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