Mack Mercer made a pair of free throws to cap Belmont's 19-4 run and the Bruins led 65-63 with 49 seconds to play. Flannigan scored a running hook shot to tie it at 65. Mercer, who scored a game-high 20 points, then missed a jumper.
The Vikings' Andre Yates took the inbound pass at midcourt with 4.3 seconds to go, and passed to Flannigan in the low post. Flannigan spun and shot a left-handed layup off the glass for the game-winner. Belmont (7-6) threw a pass down court and it was knocked down under the basket to end it.
Daniel Levitt made a 3 to give Cleveland State (4-7) a 59-46 lead with nine minutes left. Flannigan scored eight of his 16 points and had two rebounds with and a block in the final seven minutes.