It was the third championship in this tournament for the Orange (7-0), who also claimed the title in 1990 and 1998.
Baylor pulled off a big rally to edge Dayton in the semifinals on Tuesday, but could not get over the hump against Syracuse after trailing by only six with three minutes to play.
Jerami Grant scored 19 points for Syracuse while both Trevor Cooney and Tyler Ennis had 11.
Baylor shot 55 percent against the normally rugged Syracuse defense, but the Orange forced 19 turnovers.
Cory Jefferson led Baylor (6-1) with 15 points.