Boeheim, who has spent his entire 37-year coaching career at Syracuse, moved into second place by himself on the all-time victory list for major college basketball coaches.
Rutgers owned a 20-18 lead with 8 minutes to play in the first half, but Syracuse scored the final 21 points of the period. Southerland scored seven of them and finished the run with a layup that gave the Orange a 39-20 halftime lead.
Syracuse improved to 13-1 in what was the first Big East Conference game of the season for both clubs.
Brandon Triche led Syracuse with 25 points and C.J. Fair had 15. Eli Carter was the only player in double figures for Rutgers (9-3) with 19.
Rutgers coach Mike Rice returned to the bench after a three-game suspension without a pay and a $50,000 fine imposed by the school. The action was taken after an internal investigation showed a history of abusive behavior by Rice toward players during practice sessions.