Baruch led by 10 (51-41) with 8:34 left, but John Jay went on a 16-6 run the rest of the way for the comeback home win.
The Bloodhounds shot 6-of-9 down the stretch and took a three-point lead with 45 seconds.
Chris Alesi cut the deficit to one on a lay up with 37 seconds left, but Baruch (16-7, 8-3 CUNYAC) could not get any closer despite a chance to win in the final second.
Aramis Ramos led the way for John Jay (7-15, 4-7 CUNYAC) with 26 points.
Robi Davidson led the Bearcats with 13 points, while senior guard John Burzo notched his 1,000 career point and finished the game with nine points and four assists.
The men's basketball team will return to action this Wednesday with a conference home game against Hunter College. Tip Off for the Lexington Avenue Men's Basketball Classic will begin at 7:30 p.m.