The victory extended the Boilermakers' winning streak to six games. The game-winning field goal was set up by Ray Williams, who made an improbable over-the-shoulder 36-yard catch on a pass from Kyle Orton.
No. 23 Wisconsin (6-2, 3-1 Big Ten) had tied the game at 23-23 with 2:55 left when Jim Leonhard returned a punt 63 yards for a touchdown, breaking a tackle before diving into the end zone.
On Orton's pass, Williams glanced back and made a dazzling catch with Wisconsin cornerback Chuckie Cowans in hot pursuit.
The Boilermakers (6-1, 3-0) cautiously ran down the clock before Jones booted the game-winner.
Orton completed 38-of-55 passes for 410 yards and was not intercepted. Taylor Stubblefield caught 16 passes for 129 yards, and John Standeford had 14 catches for 184 yards.
Wisconsin could not overcome four turnovers and the loss of quarterback Jim Sorgi, who suffered a knee injury.