The Big Ten West-leading Wildcats (5-3, 5-1) moved 1 1/2 games ahead of the Badgers (5-3, 3-2) and gained some revenge for a loss at Camp Randall Stadium early last season that helped keep them out of the conference championship game.
With quarterback Alex Hornibrook missing the game because of a concussion and the defense without several injured starters, it was simply a rough afternoon for Wisconsin. Northwestern turned two fumbles by star running back Jonathan Taylor and another by quarterback Jack Coan into 17 points on the way to its fourth straight victory.
Thorson was a bit shaky again after struggling in a narrow win at Rutgers. He completed 17 of 30 passes for 167 yards with three interceptions against a short-handed defense. But he ran for two TDs in the first half and found Kyric McGowan for a 24-yard score in the third quarter.
Isaiah Bowser ran for 117 yards and a touchdown. He scored on a 2-yard run early in the fourth, making it 31-10 after Coan fumbled deep in Badgers territory.
Coan was 20 of 31 for 158 yards and a touchdown in his first career start.
Taylor, the nation's leading rusher, ran for just 46 yards on 11 carries after finishing with 100 or more in eight straight games.
Garrett Groshek ran for 68. But the Badgers lost for the second time in three games.
Northwestern was leading 14-10 early in the third when Wisconsin's Jack Sanborn got flagged for roughing the punter. That set up Thorson's TD pass to McGowan in the back of the end zone.
Taylor then lost his second fumble of the game when Paddy Fisher poked the ball out as he was tackled and Montre Hartage recovered at the Wisconsin 42. That led to a 26-yard field goal by Charlie Kuhbander, making it 24-10 with 2:39 left in the quarter.
The Wildcats added to their lead early in the fourth after Coan dropped the ball on a fake handoff, picked it up, scrambled and fumbled again. Bowser's 2-yard run made it 31-10.