Butler, which was in a three-way tie for first place in the Atlantic-10 heading into Wednesday's game, dropped to 7-3 and now sits a half-game behind both the Virginia Commonwealth Rams and the Saint Louis Billikens.
Charlotte had four players in double figures, and Pierria Henry led the team with 17 points. The 49ers shot 55.3 percent from the floor in the victory, improving their record to 6-4 in league play, 1-1/2 games out of first place.
The 49ers were able to keep Butler sharpshooter Rotnei Clarke from getting comfortable all night. He finished 5 of 13 from 3-point range and 5 of 14 overall. He finished with 18 points and seven rebounds.
Butler made the game late close, getting as close as 68-67 with 8.4 seconds left on a made Clarke 3-pointer. But Charlotte made its free throws to clinch the four-point win.