The second-seeded Magicians led 40-19 with 1:46 left in the first half before the Lions scored the final seven points before the break.
Paine still trailed 50-40 with 10:43 to play before going on an 11-0 run and taking a 51-50 lead on a layup by Kedric Taylor with 7:45 left.
The Lions were still up by one, at 59-58, before Chris Brown hit a jumper with 1:19 to play to give the Magicians the lead for good.
Taylor scored a game-high 20 points for Paine (16-13), Tony Baker added 14.
Naeem Gayles led LeMoyne-Owen (18-10) with 16 points. Calvin Stoudemire added 10.