Brian Brown finished with 12 points and three steals and Trey Chapman added 11 points for the Keydets (8-13, 4-6 Southern Conference), whose win was their first at home over the Bulldogs in conference play since 1996.
VMI led just 35-31 at halftime, but opened the second half on a 14-3 run, capped off by a Jordan Weethee 3-pointer. The Keydets led by as many as 20 in the second period.
Ashton Moore scored 20 to lead The Citadel (8-12, 3-6), which struggled offensively shooting just 37.5 percent with 21 turnovers.
This was VMI's second game without leading scorer QJ Peterson, who is currently on a medical furlough.