McAndrew hit five free throws in the extra period and Huffman had a 3-pointer as Brown (4-3) built a quick 80-74 lead and never trailed.
Brown had two chances to win at the end of regulation but McAndrew missed once and Huffman missed a 15-footer at the buzzer.
The Bears hit seven 3-pointers in the first half to take a 38-36 lead into intermission. Huffman had three from long range as Brown was 7-for-13 on three-pointers in the half.
Quinnpiac's DeMario Anderson hit a 3-pointer to cut the deficit to 42-41 early in the second half. Brown responded with nine straight points to take a 51-41 lead, its biggest of the game. Quinnipiac countered with an 18-4 run over the next five minutes to claim the lead 59-55. Bryan Geffen had seven points in the Bobcats' run.
Anderson led Quinnipiac with 22 points.