Choice, who had 196 yards and two TDs against Notre Dame last week, scored twice in the first quarter Saturday. Jonathan Dwyer ran for 71 yards and two TDs in relief of Choice.
Taylor Bennett was 8-of-9 for 85 yards passing for the Yellow Jackets (2-0).
Jefferson Adcock completed just 7-of-19 passes for 45 yards and Chris Evans ran for 49 yards in the loss.
Samford (1-1) recorded only 240 total yards to 498 for Georgia Tech.