Jackson, who was 5 of 11 from the field, scored eight of his points at the free throw line for the Seawolves (4-1), who were 27 of 31 from the stripe.
Forward Tommy Brenton pulled down 14 rebounds for Stony Brook, which outrebounded Canisius (3-1) 47-32 and turned 19 offensive boards to 21 second-chance points.
Stony Brook led 36-30 at halftime and pushed that lead to 54-43 behind a Dave Coley jumper with 11:18 left to play.
Coley finished with 14 points for the Seawolves, who led throughout despite shooting 39.7 percent (25 of 63) from the field.
There's nothing to suggest the Jayhawks won't end up atop the Big 12 for a 13th season in a row. But what about a return to the Final Four?
Colorado State graduate transfer John Gillon has chosen Syracuse, giving the Orange a potential starter at point guard entering the 2016-17 season.
DeSean Murray, who averaged 20.2 points as a sophomore at Presbyterian, will transfer to Auburn to play for coach Bruce Pearl.