Johnson scored the final 12 points for Winthrop - including a 3-pointer with 3:55 left for the Eagles' final field goal. He was 7 of 8 from the stripe in the last six minutes.
Armel Potter's 3-point play with six seconds left gave Charleston Southern an 82-81 lead before Johnson drove end-to-end and drew the foul.
Winthrop was 21 of 28 from the free-throw line and Charleston Southern was 10 of 10.
Patrick Wallace drained seven 3-pointers and scored a career-high 25 points for Charleston Southern (2-5, 0-1), which was 14 of 40 (35 percent) from 3-point range.