The 49ers (4-10, 1-1 Conference USA) led by two with a minute left then made 11 free throws to hold off the Eagles (3-10, 0-2). Four free throws came after Southern Miss coach Doc Sadler was given two technicals with 19 seconds to go.
Braxton Ogbueze added 17 points, including six free throws in the final minute, and Anthony Vanhook 16 on 7-of-8 shooting. The 49ers shot 54 percent, including 11 of 25 from the arc. They made only 15 of 30 free throws but were 11 of 16 late.
Kourtlin Jackson, with four 3-pointers, had 16 points to lead the Eagles, who shot 50 percent, made 12 3-pointers but had only 11 free throws, making eight.
Charlotte trailed by five at halftime but took the lead for good on Davis' 3-point play with 6:23 left.