Jones was 7 of 11 from the field as the Hawks (20-12) made 54.7 percent (29 of 53).
Kanacevic scored 16 points, grabbed 11 rebounds and had four blocks for the fifth-seeded Hawks. Saint Joseph's will play St. Bonaventure in the quarterfinals on Friday.
Langston Galloway added 18 points and C.J. Aiken and Ronald Roberts chipped in 10 points each for the Hawks, who avenged a 57-52 loss to Charlotte on Jan. 7.
Saint Joseph's opened the game on a 13-4 run behind seven points from Kanacevic, and led the entire way.
The Hawks outrebounded Charlotte 41-31 and outscored them 14-2 on the fast break.
The 12th-seeded 49ers (13-17) were led by Chris Braswell with 20 points and DeMario Mayfield with 12.