After Lavon Long made two free throws with 2:05 left to pull Siena within two the Saints didn't score again.
The Jaspers (10-10, 7-4 Metro-Atlantic) hit 6 of 8 free throws down the stretch while the Saints (8-12, 5-6) missed their last four shots, plus two free throws and had a turnover.
Shane Richards added 14 points and Ashton Pankey and Rich Williams had 13 apiece for Manhattan, which has won 8 of 11 to reach .500 for the first time this season. The Jaspers shot 54 percent and even better from 3-point range, making 60 percent (9-15). They were also 28 of 39 from the line.
Long had 20 points to lead five players in double figures. The Saints were outscored by 10 at the foul line.