Lucky Jackson caught five passes for 141 yards and a touchdown for the Hilltoppers (5-2, 4-0 Conference USA).
Cory Munson kicked field goals of 45, 32 and 48 yards to help Western Kentucky build a 23-14 lead with 5:41 left in the third quarter. Story connected with Jackson for an 8-yard TD pass to cap the scoring with 8 seconds left in the third.
The teams scored touchdowns on four of the first five possessions of the game with Chris Reynolds' 47-yard pass to Benny LeMay making it 14-all for the 49ers (2-5, 0-3) with 9 minutes left in the second quarter.
Reynolds passed for 200 yards, a touchdown and an interception, the only turnover in the game.
