The Beavers (5-7, 2-2 CUNYAC) jumped out to a 13-point advantage with 3:58 left in the first half, but the Bearcats scored the final nine points to cut the deficit to 29-25 at the intermission.
Freshman Arki Wisnu (New York, N.Y./Newtown) was a factor in the late first-half run with a jumper and lay up before the final whistle.
The Beavers regained the momentum at the start of the second half by scoring the first six points to go up comfortably, 35-25, on a lay up by James Boddie (New York, N.Y./Jane Addams) with 17:30 left.
The Bearcats (4-8, 2-1 CUNYAC) chipped away slowly at the deficit with another rally to go up permanently, 46-44, on a pair of free throws by Brian Forrestal (New York, N.Y./St. Agnes Boys) with 6:14 left.
Wisnu then hit the biggest basket of the afternoon with a 3-pointer on the next offensive trip down the court to go up, 49-44, with just under six minutes remaining.
CCNY could only get as close as four points in the final 90 seconds, as the Bearcats held on for the solid conference victory.
The Bearcats shot better from the famous Nat Holman Gymnasium with a 40 percent mark (21-52), compared to only 33 percent (20-61) by the Beavers.
Senior guard Carl Emengo (Brooklyn, N.Y./Canarsie) led the way again with 13 points and six assists, while Wisnu finished with 10 points and two steals. Junior center Phil Schatz (Middle Village, N.Y./Archbishop Molloy) missed a double-double with nine points and 10 rebounds.
CCNY was led by Froilan Vazquez (Bronx, N.Y./Cardinal Spellman) and Taleek Norman (Bronx, N.Y./Mt. San Jacinto CC) with 11 points each.
Baruch will return to action this Monday night with a conference home game against York College (8-6, 3-0 CUNYAC). Tip-off in the ARC Arena is scheduled for 7:00 pm.