Oregon took a 49-37 lead into the halftime break, but watched the lead quickly evaporate as the second-seeded Badgers used a 27-10 run in the half's first nine minutes.
Oregon responded to lead late, the last time at 75-74 after a Joseph Young three-pointer, his 29th point of the game.
But the next possession was the game's biggest, a 49 second marathon for the Badgers that included three offensive rebounds before Ben Brust put them ahead for good with a right corner three.
The Badgers put it away at the line, making 8-of-10 in the final minute of play.
Young had a shot to tie with 15 seconds remaining, but his corner three-point attempt hit the from iron.
Frustrations boiled over as Jason Callste, who scored 20 points in his final collegiate game, shoved Traevon Jackson with 0.9 seconds remaining, earning a technical to add insult to injury.
Wisconsin outscored Oregon 48-to-28 in the second half.
The offensive glass proved to be pivotal, with the Badgers grabbing 14 to just three for the Ducks.
Oregon built the large first half lead behind Young and Calliste, who had 30 of the team's first 49 points.
Mike Moser had seven points in the game's opening minutes, but once again was plagued with foul trouble and ended with 12 points and two rebounds in his final game in a Duck uniform.
Moser is one of five Duck scholarship players who played their final games for the Ducks Saturday. Although, Young may join them and forgo his final season of eligibility.
Young told the Register-Guard's Austin Meek that it'd "probably be [his] last year" if he had a good tournament. Young averaged 24 points in two tournament games.
Oregon finished the season 24-10.