Demitrius Conger added 14 points and eight rebounds, and Chris Johnson chipped in with 10 points and seven rebounds for the Bonnies (5-2).
Ahead by one, 39-38, with 12:41 left to play, St. Bonaventure finished the game on a 19-5 run to seal the victory.
With both teams shooting less than 40 percent from the field, St. Bonaventure outshot Siena (2-7) from the free-throw line. Bonnies made 11 more free throws than the Saints.
St. Bonaventure protected the ball, only turning the ball over five times compared to Siena’s 17. The Bonnies scored 14 points off of the Saints’ miscues.
Trenity Burdine led Siena with 16 points, while O.D. Anosike led them in rebounds with 14.