Sanders put the disappointment of his first team red card against Harrogate Town behind him by scoring for the Pilgrims' youth team to cut a two-goal deficit just before half-time.
United were guilty of squandering several chances and were punished by three further Halifax goals after half-time.
Boston (3-5-2): Sam Vince; Lewis Sturman, Charlie Melville, Todd Devlin; Leon Squire (Karolis Andriulionis 70), Aaron Eyett, Juris Kormis (Lemos Periera 60), Lewis McKue, Jordan Sowerby; Charley Sanders, Jordan Nuttell.