Tim Williams had 13 points and 13 rebounds for the Bulldogs (10-17, 8-6), who bounced back from their worst offensive performance of the season—a game they won, 40-33 over Wofford.
The Paladins (6-19, 3-11), who had won all five previous meetings on their home court against Samford, lost their sixth consecutive game.
Samford led by as many as nine points in the first half, but Furman cut the gap to 31-26 at halftime and gained a brief lead after a 9-2 start to the second half.
The Paladins led 40-39 before two baskets by Kelly and one by Williams put the Bulldogs in front 45-40, and they led the rest of the way.
Colin Reddick scored 14 points and Bryant Irwin 13 to lead Furman.