Dayton (15-12, 5-8) had been winless in six A10 road games. Josh Benson and Kevin Dillard added 15 points each, Vee Sanford had 13 and Dyshawn Pierre had 12 for the Flyers.
Dayton entered making a conference-leading 46.4 percent from the field in A10 games, and drained 61.7 percent (29 of 47) Wednesday, including 6 of 15 from 3-point range.
The loss was the third straight for Charlotte (18-9, 6-7). Darion Clark paced the 49ers with 17 points and Terrence Williams added 15 off the bench.
Charlotte led 34-29 at halftime, but Dayton shot 66.7 percent (18 of 27) in the second half and outscored the 49ers 59-33.
Charlotte shot 37 percent (10 of 27) after halftime, whiffing on all eight 3-point tries.