Madison finished with 14 points, while Djim Bandoumel led Idaho (8-8, 1-1) with 16 points.
Idaho had a 53-46 lead with 7:11 remaining, but Fresno State (7-10, 0-2) turned up the defensive pressure with a full-court press and the Vandals struggled to hang onto the ball.
Fresno State tied the game at 59 when Kevin Olekaibe scored a fast-break layup off a steal with 41.4 seconds remaining.
After running down the clock to six seconds, Idaho’s Deremy Geiger hoisted a shot that was too long, but Madison positioned himself for the put-back layup.
Fresno State had a chance to tie the game when Jonathan Wills set up from the outside for a shot, but he traveled for the game-sealing turnover.
The Bulldogs were led by Olekaibe’s 15 points.