The Toreros have struggled. They went into Thursday night's game at St Mary's without Trumaine Johnson who was suspended by head coach Bill Grier.
It was the 10th double-double of the season for Samhan. Diamon Simpson, the school's all-time leading rebounder, chipped in 12 rebounds to go with his nine points.
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With the victory, Saint Mary's (21-5, 8-4 West Coast) remained a half-game behind Portland in the race for second-place and a first-round bye in next month's WCC tournament.
San Diego (13-14, 5-7) trailed by as much as nine points in the second half but climbed back within two. The Toreros, who were led by Gyno Pomare's 25 points, could not get any closer, though.
They got within two at the 5:09 mark and then again on Chris Lewis' 3-pointer with 25 seconds on the clock. Mickey McConnell then hit two free throws to put Saint Mary's up by four.
Saint Mary's controlled the game early, going up by as many as seven points in the game's first 10 minutes. The crowd erupted on Ian O'Leary's alley-oop slam dunk with 9:39 to go in the half, putting the Gaels up by six and prompting a timeout from San Diego.
The Toreros came back, hitting five of their final seven shots of the first half, to take a 32-30 lead on De'Jon Jackson's layup with 41 seconds to go in the half. Diamon Simpson hit a jumper with his feet on the 3-point line at the buzzer, sending the teams into the locker room tied.
Early in the second half Saint Mary's went on a 13-4 run, capped by Carlin Hughes' steal and layup with 11:43 on the clock, to go back up by seven, 49-42. A dunk by Simpson with 8:30 to go pushed the lead to nine, 53-44.
San Diego played the game without starting guard Trumaine Johnson, who was serving a one-game suspension for an unspecified violation of team rules, according to the school. Johnson had missed the first 12 games of the season for disciplinary reasons. Since returning, he had scored in double-digits in nine of 14 games.