The victory keeps the 49ers in ninth place with three games remaining in the regular season, and knocks the Hilltoppers into a tie with Texas-San Antonio for the seventh seed.
Charlotte had lost five of its last six games coming into the contest.
The 49ers shot 45.6 percent from the field (26 of 57), including 8 of 22 from long range. But the difference came at the free throw line, where Charlotte (12-14, 6-9) hit 23 of 29 attempts — 11 more attempts than Western Kentucky (13-15, 7-8).
Davis hit 6 of 11 from the floor. Ogbueze added 16 points and Ajukwa contributed 15.
Pancake Thomas had 23 points for Western Kentucky, which shot 51.7 percent from the field (31 of 60).
