The 49ers rallied back from double-digit deficits twice in the second half only to fall in triple overtime to host St. Bonaventure, 92-88.
Jamar Briscoe and Javarris Barnett led the 49ers with 20 points each but the Bonnies Andrew Nicholson, the A-10's leading scorer, had 34 points to lead all scorers. Derrio Green added his first career points-assists double-double with 14 points and a career-high 10 assists.
SBU (9-5; 1-0) hit 31-of-42 free throws in the victory, while Charlotte hit 8-of-9.
Charlotte (8-8; 0-2) dropped its first two A-10 games of the season on the road.
"I'm proud of the guys that we haven't layed down in those situations," said 49ers head coach Alan Major. "Now, to grow, we need to make the other team be on the other end -- that's where we can continue to grow.
Charlotte trailed by 10 with 10:41 to play but used a 12-2 run bolstered by three-pointers from Barnett and Briscoe, as well as three foul shots from Briscoe to pull even. The 49ers led by two with 16 seconds left when Demitrius Conger missed two free throws. KJ Sherrill was called for a hold on the rebounds and Da'Quan Cook hit both threes to force the first OT with 12 seconds left.
In the second overtime, the 49ers had the ball with a chance to win with 5 seconds left but Green's three-pointer was off the mark. He scrambled to steal the long rebound but was called for a double-dribble to force the third OT.
In the third OT, SBU scored nine points from the foul line to pull out the victory.
Charlotte hosts Fordham, Saturday at 7:00 p.m.