Dion Wright finished with 12 points and eight rebounds while Andell Cumberbatch added 10 and seven for the Bonnies (17-12, 10-8), who won their second most games in Atlantic-10 play, and their most since the 1999-00 season.
Mandell Thomas' dunk with 15:27 remaining gave Fordham (9-20, 4-14) a 36-33 lead, but the Rams would go more than 10 minutes before making another field goal.
Ndoye scored seven, Wright six and Cumberbatch made a pair of 3-pointers during an ensuing 19-2 run which gave Saint Bonaventure a 14-point lead with 8:18 to play and Fordham trailed by at least 13 the rest of the way.
Thomas led the Rams with 20 points.
Fordham made just 19 of 54 (35 percent) field goals.