The exuberant Henderson's barrage combined with poor Wisconsin shooting to result in the upset. The Badgers hit just 15-of-59 from the field for 25.4 percent in the game.
The Rebels, who tied a school record with their 27th win against eight losses, will have a third-round game Sunday against 13th-seeded La Salle, which beat Kansas State 63-61 later Friday.
That result assures a double-digit-seeded team will reach the tournament's fourth round.
Sam Dekker hit a shot that put Wisconsin (23-12) up 36-30 with about 12 minutes to go but Henderson answered with two 3-point shots, setting off a 27-10 Rebels run the rest of the way. The Badgers managed just seven points over the final 9 minutes.
Henderson started slowly, with three points in the first half, but ended with a game-high 19 on 6-of-21 -- 3-of-12 from 3-point range -- shooting. Murphy Holloway, whose back-to-back shots erased the final Wisconsin lead, ended with 10 points.
Sam Dekker scored 14 points as the only Wisconsin player in double figures.