Trevor Lacey added 11 points for the Crimson Tide (22-12), who out-rebounded the Huskies (20-13) 37-27 and scored 36 points in the paint to 14 for the visitors.
Alabama will face fourth-seeded Stanford in the second round.
Alabama opened the game with a 17-3 run and led 28-23 at halftime.
Northeastern (20-13) played without injured leading scorer Joel Smith and struggled with a 33.3 percent shooting average. Jonathan Lee was high scorer for the Huskies with 13 points.